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Galaxy Tool XML File

The XML File for a Galaxy tool, generally referred to as the “tool config file” or “wrapper”, serves a number of purposes. First, it lays out the user interface for the tool (e.g. form fields, text, help, etc.). Second, it provides the glue that links your tool to Galaxy by telling Galaxy how to invoke it, what options to pass, and what files it will produce as output.

If you find a bug please report it here.

This document serves as reference documentation. If you would like to learn how to build tools for Galaxy, Planemo features a number of tutorials on building Galaxy tools that would better serve that purpose.

tool

The outer-most tag set of tool XML files. Attributes on this tag apply to the tool as a whole.

Examples

A normal tool:

<tool id="seqtk_seq"
      name="Convert FASTQ to FASTA"
      version="1.0.0"
      profile="16.04"
>

A data_source tool contains a few more relevant attributes.

<tool id="ucsc_table_direct1"
      name="UCSC Main"
      version="1.0.0"
      hidden="false"
      profile="16.01"
      tool_type="data_source"
      URL_method="post">

Best Practices

Find the Intergalactic Utilities Commision suggested best practices for this element here.

Attributes

Attribute	Details	Required
id	Must be unique across all tools; should be lowercase and contain only letters, numbers, and underscores. It allows for tool versioning and metrics of the number of times a tool is used, among other things. Find the Intergalactic Utilities Commision suggested best practices for this element here.	True
name	This string is what is displayed as a hyperlink in the tool menu. Find the Intergalactic Utilities Commision suggested best practices for this element here _.	True
version	This string defaults to 1.0.0 if it is not included in the tag. It allows for tool versioning and should be increased with each new version of the tool. Find the Intergalactic Utilities Commision suggested best practices for this element `here <https://planem o.readthedocs.io/en/l atest/standards/docs/ best_practices/tool_x ml.html#tool-versions >`__.	False
hidden	Allows for tools to be loaded upon server startup, but not displayed in the tool menu. This attribute should be applied in the toolbox configuration instead and so should be considered deprecated.	False
display_interface	Disable the display the tool’s graphical tool form by setting this to false.	False
tool_type	Allows for certain framework functionality to be performed on certain types of tools. Normal tools that execute typical command-line jobs do not need to specify this, special kinds of tools such as `Data Source <https://galax yproject.org/admin/in ternals/data-sources/ >`__ and Data Manager <https://gala xyproject.org/admin/t ools/data-managers/> __ tools should set this to have values such as data_source or manage_data.	False
profile	This string specified the minimum Galaxy version that should be required to run this tool. Certain legacy behaviors such as using standard error content to detect errors instead of exit code are disabled automatically if profile is set to any version newer than 16.01, such as 16.04.	False
``workflow_compatible ``	This attribute indicates if this tool is usable within a workflow (defaults to true for normal tools and false for data sources).	False
URL_method	Only used if tool_type attribute value is data_source - this attribute defines the HTTP request method to use when communicating with an external data source application (the default is get).	False

tool > description

The value is displayed in the tool menu immediately following the hyperlink for the tool (based on the name attribute of the <tool> tag set described above).

Example

<description>table browser</description>

Best Practices

Find the Intergalactic Utilities Commision suggested best practices for this element here.

tool > macros

Frequently, tools may require the same XML fragments be repeated in a file (for instance similar conditional branches, repeated options, etc…) or among tools in the same repository. Galaxy tools have a macro system to address this problem.

For more information, see https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements

tool > edam_topics

Container tag set for the <edam_topic> tags. A tool can have any number of EDAM topic references.

<!-- Example: this tool is about 'Statistics and probability' (http://edamontology.org/topic_2269) -->
<edam_topics>
    <edam_topic>topic_2269</edam_topic>
</edam_topics>

tool > edam_operations

Container tag set for the <edam_operation> tags. A tool can have any number of EDAM operation references.

<!-- Example: this tool performs a 'Conversion' operation (http://edamontology.org/operation_3434) -->
<edam_operations>
    <edam_operation>operation_3434</edam_operation>
</edam_operations>

tool > requirements

This is a container tag set for the requirement and container tags described in greater detail below. requirements describe software packages and other individual computing requirements required to execute a tool, while containers describe Docker containers that should be able to serve as complete descriptions of the runtime of a tool.

tool > requirements > requirement

This tag set is contained within the requirements tag set. Third party programs or modules that the tool depends upon are included in this tag set.

When a tool runs, Galaxy attempts to resolve these requirements (also called dependencies). requirements are meant to be abstract and resolvable by multiple different systems (e.g. conda, the Galaxy Tool Shed dependency management system, or environment modules).

Read more about dependency resolvers in Galaxy on docs.galaxyproject.org. The current best practice for tool dependencies is to target Conda, this is discussed in greater detail here.

Examples

This example shows a tool that requires the samtools 0.0.18 package.

This package is available via the Tool Shed (see Tool Shed dependency management ) as well as Conda and can be configured locally to adapt to any other package management system.

<requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
</requirements>

This older example shows a tool that requires R version 2.15.1. The tool_depensencies.xml should contain matching declarations for Galaxy to actually install the R runtime. The set_envirornment type is only respected by the tool shed and is ignored by the newer and preferred conda dependency resolver.

<requirements>
    <requirement type="set_environment">R_SCRIPT_PATH</requirement>
    <requirement type="package" version="2.15.1">R</requirement>
</requirements>

Attributes

Attribute	Details	Required
type	This value defines the which type of the 3rd party module required by this tool.	True
version	For package type requirements this value defines a specific version of the tool dependency.	False

tool > requirements > container

This tag set is contained within the ‘requirements’ tag set. Galaxy can be configured to run tools within Docker containers - this tag allows the tool to suggest possible valid Docker containers for this tool.

Read more about configuring Galaxy to run Docker jobs here.

Attributes

Attribute	Details	Required
type	This value describes the type of container that the tool may be executed in and currently must be docker.	True

tool > code

Deprecated Do not use this unless absolutely necessary.

The extensions described here can cause problems using your tool with certain components of Galaxy (like the workflow system). It is highly recommended to avoid these constructs unless absolutely necessary.

This tag set provides detailed control of the way the tool is executed. This (optional) code can be deployed in a separate file in the same directory as the tool’s config file. These hooks are being replaced by new tool config features and methods in the /lib/galaxy/tools/__init__.py code file.

Examples

Dynamic Options

Use associated dynamic select lists where selecting an option in the first select list dynamically re-renders the options in the second select list. In this example, we are populating both dynamic select lists from metadata elements associated with a tool’s single input dataset. The 2 metadata elements we’re using look like this.

MetadataElement(name="field_names", default=[], desc="Field names", readonly=True, optional=True, visible=True, no_value=[])
# The keys in the field_components map to the list of field_names in the above element
# which ensures order for select list options that are built from it.
MetadataElement(name="field_components", default={}, desc="Field names and components", readonly=True, optional=True, visible=True, no_value={})

Our tool config includes a code file tag like this.

<code file="tool_form_utils.py" />

Here are the relevant input parameters in our tool config. The first parameter is the input dataset that includes the above metadata elements.

<param name="input" type="data" format="vtkascii,vtkbinary" label="Shape with uncolored surface field">
    <validator type="expression" message="Shape must have an uncolored surface field.">value is not None and len(value.metadata.field_names) > 0</validator>
</param>

The following parameter dynamically renders a select list consisting of the elements in the field_names metadata element associated with the selected input dataset.

<param name="field_name" type="select" label="Field name" refresh_on_change="true">
    <options>
        <filter type="data_meta" ref="input" key="field_names"/>
        <validator type="no_options" message="The selected shape has no uncolored surface fields." />
    </options>
</param>

The following parameter calls the get_field_components_options() function in the tool_form_utils.py code file discussed above. This function returns the value of the input dataset’s field_components metadata element dictionary whose key is the currently selected field_name from the select list parameter above.

<param name="field_component_index" type="select" label="Field component index" dynamic_options="get_field_components_options(input, field_name=field_name)" help="Color will be applied to the selected field's component associated with this index." />

Changing the selected option in the field_name select list will dynamically re-render the options available in the associated field_component_index select list, which is the behavior we want.

The get_field_components_options() method looks like this.

def get_field_components_options(dataset, field_name):
    options = []
    if dataset.metadata is None:
        return options
    if not hasattr(dataset.metadata, 'field_names'):
        return options
    if dataset.metadata.field_names is None:
        return options
    if field_name is None:
        # The expression validator that helps populate the select list of input
        # datsets in the icqsol_color_surface_field tool does not filter out
        # datasets with no field field_names, so we need this check.
        if len(dataset.metadata.field_names) == 0:
            return options
        field_name = dataset.metadata.field_names[0]
    field_components = dataset.metadata.field_components.get(field_name, [])
    for i, field_component in enumerate(field_components):
        options.append((field_component, field_component, i == 0))
    return options

Parameter Validation

This function is called before the tool is executed. If it raises any exceptions the tool execution will be aborted and the exception’s value will be displayed in an error message box. Here is an example:

def validate(incoming):
    """Validator for the plotting program"""


    bins = incoming.get("bins","")
    col = incoming.get("col","")


    if not bins or not col:
        raise Exception, "You need to specify a number for bins and columns"


    try:
        bins = int(bins)
        col = int(col)
    except:
        raise Exception, "Parameters are not integers, columns:%s, bins:%s" % (col, bins)


    if not 1<bins<100:
        raise Exception, "The number of bins %s must be a number between 1 and 100" % bins

This code will intercept a number of parameter errors and return corresponding error messages. The parameter incoming contains a dictionary with all the parameters that were sent through the web.

Pre-job and pre-process code

The signature of both of these is the same:

def exec_before_job(inp_data, out_data, param_dict, tool):
def exec_before_process(inp_data, out_data, param_dict, tool):

The param_dict is a dictionary that contains all the values in the incoming parameter above plus a number of keys and values generated internally by galaxy. The inp_data and the out_data are dictionaries keyed by parameter name containing the classes that represent the data.

Example:

def exec_before_process(inp_data, out_data, param_dict, tool):
    for name, data in out_data.items():
        data.name = 'New name'

This custom code will change the name of the data that was created for this tool to New name. The difference between these two functions is that the exec_before_job executes before the page returns and the user will see the new name right away. If one were to use exec_before_process the new name would be set only once the job starts to execute.

Post-process code

This code executes after the background process running the tool finishes its run. The example below is more advanced one that replaces the type of the output data depending on the parameter named extension:

from galaxy import datatypes
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
    ext = param_dict.get('extension', 'text')
    items = out_data.items()
    for name, data in items:
        newdata = datatypes.factory(ext)(id=data.id)
        for key, value in data. __dict__.items():
            setattr(newdata, key, value)
        newdata.ext = ext
        out_data[name] = newdata

The content of stdout and stderr are strings containing the output of the process.

Attributes

Attribute	Details	Required
file	This value is the name of the executable code file, and is called in the exec_before_process (), exec_before_job() , exec_after_process( ) and exec_after_job() methods.	True

tool > stdio

Tools write the bulk of useful data to datasets, but they can also write messages to standard I/O (stdio) channels known as standard output (stdout) and standard error (stderr). Both stdout and stderr are typically written to the executing program’s console or terminal. Previous versions of Galaxy checked stderr for execution errors - if any text showed up on stderr, then the tool’s execution was marked as failed. However, many tools write messages to stderr that are not errors, and using stderr allows programs to redirect other interesting messages to a separate file. Programs may also exit with codes that indicate success or failure. One convention is for programs to return 0 on success and a non-zero exit code on failure.

Legacy tools (ones with profile unspecified or a profile of less than 16.04) will default to checking stderr for errors as described above. Newer tools will instead treat an exit code other than 0 as an error. The detect_error on command can swap between these behaviors but the stdio directive allows more options in defining error conditions (though these aren’t always intuitive).

With stdio directive, Galaxy can use regular expressions to scan stdout and stderr, and it also allows exit codes to be scanned for ranges. The <stdio> tag has two subtags, <regex> and <exit_code>, to define regular expressions and exit code processing, respectively. They are defined below. If a tool does not have any valid <regex> or <exit_code> tags, then Galaxy will use the previous technique for finding errors.

A note should be made on the order in which exit codes and regular expressions are applied and how the processing stops. Exit code rules are applied before regular expression rules. The rationale is that exit codes are more clearly defined and are easier to check computationally, so they are applied first. Exit code rules are applied in the order in which they appear in the tool’s configuration file, and regular expressions are also applied in the order in which they appear in the tool’s configuration file. However, once a rule is triggered that causes a fatal error, no further rules are checked.

tool > stdio > exit_code

Tools may use exit codes to indicate specific execution errors. Many programs use 0 to indicate success and non-zero exit codes to indicate errors. Galaxy allows each tool to specify exit codes that indicate errors. Each tag defines a range of exit codes, and each range can be associated with a description of the error (e.g., “Out of Memory”, “Invalid Sequence File”) and an error level. The description just describes the condition and can be anything. The error level is either a warning or a fatal error. A warning means that stderr will be updated with the error’s description. A fatal error means that the tool’s execution will be marked as having an error and the workflow will stop. Note that, if the error level is not supplied, then a fatal error is assumed to have occurred.

The exit code’s range can be any consecutive group of integers. More advanced ranges, such as noncontiguous ranges, are currently not supported. Ranges can be specified in the form “m:n”, where m is the start integer and n is the end integer. If “:n” is specified, then the exit code will be compared against all integers less than or equal to n. If “m:” is used, then the exit code will be compared against all integers greater than or equal to m. If the exit code matches, then the error level is applied and the error’s description is added to stderr. If a tool’s exit code does not match any of the supplied tags’ ranges, then no errors are applied to the tool’s execution.

Note that most Unix and Linux variants only support positive integers 0 to 255 for exit codes. If an exit code falls out of the range 0 to 255, the usual convention is to only use the lower 8 bits for the exit code. The only known exception is if a job is broken into subtasks using the tasks runner and one of those tasks is stopped with a POSIX signal. (Note that signals should be used as a last resort for terminating processes.) In those cases, the task will receive -1 times the signal number. For example, suppose that a job uses the tasks runner and 8 tasks are created for the job. If one of the tasks hangs, then a sysadmin may choose to send the “kill” signal, SIGKILL, to the process. In that case, the task (and its job) will exit with an exit code of -9. More on POSIX signals can be found at https://en.wikipedia.org/wiki/Unix_signal as well as man pages on “signal”.

The tag’s supported attributes are as follows:

• range: This indicates the range of exit codes to check. The range can be one of the following:
  • n: the exit code will only be compared to n;
  • [m:n]: the exit code must be greater than or equal to m and less than or equal to n;
  • [m:]: the exit code must be greater than or equal to m;
  • [:n]: the exit code must be less than or equal to n.
• level: This indicates the error level of the exit code. The level can have one of two values:
  • warning: If an exit code falls in the given range, then a description of the error will be added to the beginning of stderr. A warning-level error will not cause the tool to fail.
  • fatal: If an exit code falls in the given range, then a description of the error will be added to the beginning of stderr. A fatal-level error will cause the tool to fail. If no level is specified, then the fatal error level will be assumed to have occurred.
• description: This is an optional description of the error that corresponds to the exit code.

The following is an example of the tag:

<stdio>
    <exit_code range="3:5" level="warning" description="Low disk space" />
    <exit_code range="6:"  level="fatal"   description="Bad input dataset" />
    <!-- Catching fatal_oom allows the job runner to potentially resubmit to a resource with more
         memory if Galaxy is configured to do this. -->
    <exit_code range="2"   level="fatal_oom"   description="Out of Memory" />
</stdio>

If the tool returns 0 or 1, then the tool will not be marked as having an error. If the exit code is 2, then the tool will fail with the description Out of Memory added to stderr. If the tool returns 3, 4, or 5, then the tool will not be marked as having failed, but Low disk space will be added to stderr. Finally, if the tool returns any number greater than or equal to 6, then the description Bad input dataset will be added to stderr and the tool will be marked as having failed.

tool > stdio > regex

A regular expression defines a pattern of characters. The patterns include the following:

• GCTA, which matches on the fixed string “GCTA”;
• [abcd], which matches on the characters a, b, c, or d;
• [CG]{12}, which matches on 12 consecutive characters that are C or G;
• a.*z, which matches on the character “a”, followed by 0 or more characters of any type, followed by a “z”;
• ^X, which matches the letter X at the beginning of a string;
• Y$, which matches the letter Y at the end of a string.

There are many more possible regular expressions. A reference to all supported regular expressions can be found under Python Regular Expression Syntax.

A regular expression includes the following attributes:

• source: This tells whether the regular expression should be matched against stdout, stderr, or both. If this attribute is missing or is incorrect, then both stdout and stderr will be checked. The source can be one of the follwing values:
  • stdout: the regular expression will be applied to stdout;
  • stderr: the regular expression will be applied to stderr;
  • both: the regular expression will be applied to both stderr and stdout (which is the default case).
• match: This is the regular expression that will be used to match against stdout and/or stderr. If the tag does not contain the match attribute, then the tag will be ignored. The regular expression can be any valid Python regular expression. All regular expressions are performed case insensitively. For example, if match contains the regular expression “actg”, then the regular expression will match against “actg”, “ACTG”, “AcTg”, and so on. Also note that, if double quotes (“) are to be used in the match attribute, then the value ” can be used in place of double quotes. Likewise, if single quotes (‘) are to be used in the match attribute, then the value ‘ can be used if necessary.
• level: This works very similarly to the tag, except that, when a regular expression matches against its source, the description is added to the beginning of the source. For example, if stdout matches on a regular expression, then the regular expression’s description is added to the beginning of stdout (instead of stderr). The level can be log, warning or fatal as described below.
• log and warning: If the regular expression matches against its source input (i.e., stdout and/or stderr), then a description of the error will be added to the beginning of the source, prepended with either ‘Log:’ or ‘Warning:’. A log-level/warning-level error will not cause the tool to fail.
• fatal: If the regular expression matches against its source input, then a description of the error will be added to the beginning of the source. A fatal-level error will cause the tool to fail. If no level is specified, then the fatal error level will be assumed to have occurred.
• description: Just like its exit_code counterpart, this is an optional description of the regular expression that has matched.

The following is an example of regular expressions that may be used:

<stdio>
    <regex match="low space"
           source="both"
           level="warning"
           description="Low space on device" />
    <regex match="error"
           source="stdout"
           level="fatal"
           description="Unknown error encountered" />
    <!-- Catching fatal_oom allows the job runner to potentially resubmit to a resource with more
         memory if Galaxy is configured to do this. -->
    <regex match="out of memory"
           source="stdout"
           level="fatal_oom"
           description="Out of memory error occurred" />
    <regex match="[CG]{12}"
           description="Fatal error - CG island 12 nts long found" />
    <regex match="^Branch A"
           level="warning"
           description="Branch A was taken in execution" />
</stdio>

The regular expression matching proceeds as follows. First, if either stdout or stderr match on low space, then a warning is registered. If stdout contained the string ---LOW SPACE---, then stdout has the string Warning: Low space on device added to its beginning. The same goes for if stderr had contained the string low space. Since only a warning could have occurred, the processing continues.

Next, the regular expression error is matched only against stdout. If stdout contains the string error regardless of its capitalization, then a fatal error has occurred and the processing stops. In that case, stdout would be prepended with the string Fatal: Unknown error encountered. Note that, if stderr contained error, ERROR, or ErRor then it would not matter - stderr was not being scanned.

If the second regular expression did not match, then the third regular expression is checked. The third regular expression does not contain an error level, so an error level of fatal is assumed. The third regular expression also does not contain a source, so both stdout and stderr are checked. The third regular expression looks for 12 consecutive “C”s or “G”s in any order and in uppercase or lowercase. If stdout contained cgccGGCCcGGcG or stderr contained CCCCCCgggGGG, then the regular expression would match, the tool would be marked with a fatal error, and the stream that contained the 12-nucleotide CG island would be prepended with Fatal: Fatal error - CG island 12 nts long found.

Finally, if the tool did not match any of the fatal errors, then the fourth regular expression is checked. Since no source is specified, both stdout and stderr are checked. If Branch A is at the beginning of stdout or stderr, then a warning will be registered and the source that contained Branch A will be prepended with the warning Warning: Branch A was taken in execution.

tool > version_command

Specifies the command to be run in order to get the tool’s version string. The resulting value will be found in the “Info” field of the history dataset.

Unlike the command tag, with the exception of the string $__tool_directory__ this value is taken as a literal and so there is no need to escape values like $ and command inputs are not available for variable substitution.

Examples

A simple example for a TopHat tool definition might just be:

<version_command>tophat -version</version_command>

An example that leverages a Python script (e.g. count_reads.py) shipped with the tool might be:

<version_command>python '$__tool_directory__/count_reads.py'</version_command>

Examples are included in the test tools directory including:

• version_command_plain.xml
• version_command_tool_dir.xml
• version_command_interpreter.xml (deprecated)

Attributes

Attribute	Details	Required
interpreter	Deprecated: Prefix the version command with an interpreter and the tool directory in order to execute a script shipped with the tool. It is better to just use <interpreter> '$__t ool_directory__/<scri pt_name>'.	False

tool > command

This tag specifies how Galaxy should invoke the tool’s executable, passing its required input parameter values (the command line specification links the parameters supplied in the form with the actual tool executable). Any word inside it starting with a dollar sign ($) will be treated as a variable whose values can be acquired from one of three sources: parameters, metadata, or output files. After the substitution of variables with their values, the content is interpreted with Cheetah and finally given to the interpreter specified in the corresponding attribute (if any).

Examples

The following uses a compiled executable (bedtools).

<command>bed12ToBed6 -i '$input' > '$output'</command>

A few things to note about even this simple example:

• Input and output variables (boringly named input and output) are expanded into paths using the $ Cheetah directive.
• Paths should be quoted so that the Galaxy database files may contain spaces.
• We are building up a shell script - so special characters like > can be used (in this case the standard output of the bedtools call is written to the path specified by '$output').

The bed12ToBed6 tool can be found here.

A more sophisticated bedtools example demonstrates the use of loops, conditionals, and uses whitespace to make a complex command very readable can be found in annotateBed tool.

<command><![CDATA[
bedtools annotate
        -i "${inputA}"
        #if $names.names_select == 'yes':
            -files
            #for $bed in $names.beds:
                '${bed.input}'
            #end for
            -names
            #for $bed in $names.beds:
                '${bed.inputName}'
            #end for
        #else:
            #set files = '" "'.join([str($file) for $file in $names.beds])
            -files '${files}'
            #set names = '" "'.join([str($name.display_name) for $name in $names.beds])
            -names '${names}'
        #end if
        $strand
        $counts
        $both
        > "${output}"
]]></command>

The following example (taken from xpath tool) uses an interpreted executable. In this case a Perl script is shipped with the tool and the directory of the tool itself is referenced with $__tool_directory__.

<command><![CDATA[
perl '$__tool_directory__/xpath' -q -e '$expression' '$input' > '$output'
]]></command>

The following example demonstrates accessing metadata from datasets. Metadata values (e.g., ${input.metadata.chromCol}) are acquired from the Metadata model associated with the objects selected as the values of each of the relative form field parameters in the tool form. Accessing this information is generally enabled using the following feature components.

A set of “metadata information” is defined for each supported data type (see the MetadataElement objects in the various data types classes in /lib/galaxy/datatypes. The DatasetFilenameWrapper class in the /lib/galaxy/tools/wrappers.py code file wraps a metadata collection to return metadata parameters wrapped according to the Metadata spec.

<command><![CDATA[
        #set genome = $input.metadata.dbkey
        #set datatype = $input.datatype
        mkdir -p output_dir &&
        python '$__tool_directory__/extract_genomic_dna.py'
        --input '$input'
        --genome '$genome'
        #if $input.is_of_type("gff"):
            --input_format "gff"
            --columns "1,4,5,7"
            --interpret_features $interpret_features
        #else:
            --input_format "interval"
            --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
        #end if
        --reference_genome_source $reference_genome_cond.reference_genome_source
        #if str($reference_genome_cond.reference_genome_source) == "cached"
            --reference_genome $reference_genome_cond.reference_genome.fields.path
        #else:
            --reference_genome $reference_genome_cond.reference_genome
        #end if
        --output_format $output_format_cond.output_format
        #if str($output_format_cond.output_format) == "fasta":
            --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
            #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
                --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
            #end if
        #end if
        --output '$output'
]]></command>

In additon to demonstrating accessing metadata, this example demonstrates:

• $input.is_of_type("gff") which can be used to check if an input is of a given datatype.
• #set datatype = $input.datatype which is the syntax for defining variables in Cheetah.

Reserved Variables

Galaxy provides a few pre-defined variables which can be used in your command line, even though they don’t appear in your tool’s parameters.

Name	Description
$__tool_direct ory__	The directory the tool description (XML file) currently resides in (new in 15.03)
$__new_file_pa th__	config/galaxy.ini’s new_file_path value
$__tool_data_p ath__	config/galaxy.ini’s tool_data_path value
``$__root_dir__` `	Top-level Galaxy source directory made absolute via os.path.abspath()
$__datatypes_c onfig__	config/galaxy.ini’s datatypes_config value
$__user_id__	Email’s numeric ID (id column of galaxy_user table in the database)
$__user_email_ _	User’s email address
$__app__	The galaxy.app.UniverseApplication instance, gives access to all other configuration file variables (e.g. $app.config.output_size_limit). Should be used as a last resort, may go away in future releases.

Additional runtime properties are available as environment variables. Since these are not Cheetah variables (the values aren’t available until runtime) these should likely be escaped with a backslash (\) when appearing in command or configfile elements.

Name	Description
\${GALAXY_SLOT S:-4}	Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime).
\$GALAXY_MEMOR Y_MB	Amount of memory in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.

See the Planemo docs on the topic of GALAXY_SLOTS for more information and examples.

Attributes

detect_errors

If present on the command tag, this attribute can be one of:

• default no-op fallback to stdio tags and erroring on standard error output (for legacy tools).
• exit_code error if tool exit code is not 0. (The @jmchilton recommendation).
• aggressive error if tool exit code is not 0 or Exception:, Error:, or various messages related to being out of memory appear in the standard error or output. (The @bgruening recommendation).

For newer tools with profile>=16.04, the default behavior is exit_code. Legacy tools default to default behavior described above (erroring if the tool produces any standard error output).

See pull request 117 for more implementation information and discussion on the detect_errors attribute.

strict

This boolean forces the #set -e directive on in shell scripts - so that in a multi-part command if any part fails the job exits with a non-zero exit code. This is enabled by default for tools with profile>=16.04 and disabled on legacy tools.

interpreter

Older tools may define an intepreter attribute on the command, but this is deprecated and using the $__tool_directory__ variable is superior.

Best Practices

Find the Intergalactic Utilities Commision suggested best practices for this element here.

tool > environment_variables

This directive should contain one or more environment_variable definition.

tool > environment_variables > environment_variable

This directive defines an environment variable that will be available when the tool executes. The body should be a Cheetah template block that may reference the tool’s inputs as demonstrated below.

Example

The following demonstrates a couple environment_variable definitions.

<environment_variables>
    <environment_variable name="INTVAR">$inttest</environment_variable>
    <environment_variable name="IFTEST">#if int($inttest) == 3
ISTHREE
#else#
NOTTHREE
#end if#</environment_variable>
    </environment_variables>
</environment_variables>

If these environment variables are used in another Cheetah context, such as in the command block, the $ used indicate shell expansion of a variable should be escaped with a \ so prevent it from being evaluated as a Cheetah variable instead of shell variable.

<command>
    echo "\$INTVAR"  >  $out_file1;
    echo "\$IFTEST"  >> $out_file1;
</command>

Attributes

Attribute	Details	Required
name	Name of the environment variable to define.	False

tool > configfiles

See xy_plot.xml for an example of how this tag set is used in a tool. This tag set is a container for <configfile> and <inputs> tag sets - which can be used to setup configuration files for use by tools.

tool > configfiles > configfile

This tag set is contained within the <configfiles> tag set. It allows for the creation of a temporary file for file-based parameter transfer.

Example

The following is taken from the xy_plot.xml tool config.

<configfiles>
    <configfile name="script_file">
      ## Setup R error handling to go to stderr
      options(show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr()); q("no", 1, F) })
      ## Determine range of all series in the plot
      xrange = c(NULL, NULL)
      yrange = c(NULL, NULL)
      #for $i, $s in enumerate($series)
          s${i} = read.table("${s.input.file_name}")
          x${i} = s${i}[,${s.xcol}]
          y${i} = s${i}[,${s.ycol}]
          xrange = range(x${i}, xrange)
          yrange = range(y${i}, yrange)
      #end for
      ## Open output PDF file
      pdf("${out_file1}")
      ## Dummy plot for axis / labels
      plot(NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}")
      ## Plot each series
      #for $i, $s in enumerate($series)
          #if $s.series_type['type'] == "line"
              lines(x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col})
          #elif $s.series_type.type == "points"
              points(x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col})
          #end if
      #end for
      ## Close the PDF file
      devname = dev.off()
    </configfile>
</configfiles>

This file is then used in the command block of the tool as follows:

<command>bash '$__tool_directory__/r_wrapper.sh' '$script_file'</command>

Attributes

Attribute	Details	Required
name	Cheetah variable used to reference the path to the file created with this directive.	False

tool > configfiles > inputs

This tag set is contained within the tag set. It tells Galaxy to write out a JSON representation of the tool parameters .

Example

The following will create a cheetah variable that can be evaluated as $inputs that will contain the tool parameter inputs.

<configfiles>
    <inputs name="inputs" />
<configfiles>

The following will instead write the inputs to the tool’s working directory with the specified name (i.e. inputs.json).

<configfiles>
    <inputs name="inputs" filename="inputs.json" />
<configfiles>

A contrived example of a tool that uses this is the test tool inputs_as_json.xml.

Attributes

Attribute	Details	Required
name	Cheetah variable to populate the path to the inputs JSON file created in response to this directive.	False
filename	Path relative to the working directory of the tool for the inputs JSON file created in response to this directive.	False

tool > inputs

Consists of all elements that define the tool’s input parameters. Each param element contained in this element can be used as a command line parameter within the command text content. Most tools will not need to specify any attributes on this tag itself.

Attributes

Attribute	Details	Required
action	URL used by data source tools.	False
check_values	Set to false to disable parameter checking in data source tools.	False
method	Data source HTTP action (e.g. get or put) to use.	False
target	UI link target to use for data source tools (e.g. _top).	False
nginx_upload	This boolean indicates if this is an upload tool or not.	False

tool > inputs > section

This tag is used to group parameters into sections of the interface. Sections are implemented to replace the commonly used tactic of hiding advanced options behind a conditional, with sections you can easily visually group a related set of options.

Example

The XML configuration is relatively trivial for sections:

<inputs>
    <section name="adv" title="Advanced Options" expanded="false">
        <param name="plot_color" type="color" label="Track color" />
    </section>
</inputs>

In your command template, you’ll need to include the section name to access the variable:

--color $adv.plot_color

Further examples can be found in the test case from pull request #35.

Attributes

Attribute	Details	Required
name	The internal key used for the section.	True
title	Human readable label for the section.	True
expanded	Whether the section should be expanded by default or not. If not, the default set values are used.	False
help	Short help description for section, rendered just below the section.	False

tool > inputs > repeat

See xy_plot.xml for an example of how to use this tag set. This is a container for any tag sets that can be contained within the <inputs> tag set. When this is used, the tool will allow the user to add any number of additional sets of the contained parameters (an option to add new iterations will be displayed on the tool form). All input parameters contained within the <repeat> tag can be retrieved by enumerating over $<name_of_repeat_tag_set> in the relevant Cheetah code. This returns the rank and the parameter objects of the repeat container. See the Cheetah code below.

Example

This part is contained in the <inputs> tag set.

<repeat name="series" title="Series">
    <param name="input" type="data" format="tabular" label="Dataset"/>
    <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
    <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
</repeat>

This Cheetah code can be used in the <command> tag set or the <configfile> tag set.

#for $i, $s in enumerate($series)
    rank_of_series=$i
    input_path='${s.input}'
    x_colom=${s.xcol}
    y_colom=${s.ycol}
#end for

Testing

This is an example test case with multiple repeat elements for the example above.

<test>
    <repeat name="series">
        <param name="input" value="tabular1.tsv" ftype="tabular"/>
        <param name="xcol" value="1"/>
        <param name="ycol" value="2"/>
    </repeat>
    <repeat name="series">
        <param name="input" value="tabular2.tsv" ftype="tabular"/>
        <param name="xcol" value="4"/>
        <param name="ycol" value="2"/>
    </repeat>
    <output name="out_file1" file="cool.pdf" ftype="pdf" />
</test>

See the documentation on the repeat test directive.

An older way to specify repeats in a test is by instances that are created by referring to names with a special format: “_|”

<test>
    <param name="series_0|input" value="tabular1.tsv" ftype="tabular"/>
    <param name="series_0|xcol" value="1"/>
    <param name="series_0|ycol" value="2"/>
    <param name="series_1|input" value="tabular2.tsv" ftype="tabular"/>
    <param name="series_1|xcol" value="4"/>
    <param name="series_1|ycol" value="2"/>
    <output name="out_file1" file="cool.pdf" ftype="pdf" />
</test>

The test tool disambiguate_repeats.xml demonstrates both testing strategies.

Attributes

Attribute	Details	Required
name	Name for this element	False
title	The title of the repeat section, which will be displayed on the tool form.	True
min	The minimum number of repeat units.	False
max	The maximum number of repeat units.	False
default	The default number of repeat units.	False
help	Short help description for repeat element.	False

tool > inputs > conditional

This is a container for conditional parameters in the tool (must contain ‘when’ tag sets) - the command line (or portions thereof) are then wrapped in an if-else statement. A good example tool that demonstrates many conditional parameters is biom_convert.xml.

<conditional name="input_type">
    <param name="input_type_selector" type="select" label="Choose the source BIOM format">
        <option value="tsv" selected="true">Tabular File</option>
        <option value="biom">BIOM File</option>
    </param>
    <when value="tsv">
        <param name="input_table" type="data" format="tabular" label="Tabular File" argument="--input-fp"/>
        <param name="process_obs_metadata" type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata">
            <option value="" selected="true">Do Not process metadata</option>
            <option value="taxonomy">taxonomy</option>
            <option value="naive">naive</option>
            <option value="sc_separated">sc_separated</option>
        </param>
    </when>
    <when value="biom">
        <param name="input_table" type="data" format="biom1" label="Tabular File" argument="--input-fp"/>
    </when>
</conditional>

The first directive following the conditional is a param, this param must be of type select or boolean. Depending on the value a user selects for this “test” parameter - different UI elements will be shown. These different paths are described by the following the when blocks shown above.

The following Cheetah block demonstrates the use of the conditional shown above:

biom convert -i "${input_type.input_table}" -o "${output_table}"
#if str($input_type.input_type_selector) == "tsv":
    #if $input_type.process_obs_metadata:
        --process-obs-metadata "${input_type.process_obs_metadata}"
    #end if
#end if

Notice that the parameter input_table appears down both when clauses so ${input_type.input_table} appears unconditionally but we need to conditionally reference ${input_type.process_obs_metadata} with a Cheetah if statement.

A common use of the conditional wrapper is to select between reference data managed by the Galaxy admins (for instance via data managers ) and history files. A good example tool that demonstrates this is the Bowtie 2 wrapper.

<conditional name="reference_genome">
  <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
    <option value="indexed">Use a built-in genome index</option>
    <option value="history">Use a genome from the history and build index</option>
  </param>
  <when value="indexed">
    <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
      <options from_data_table="bowtie2_indexes">
        <filter type="sort_by" column="2"/>
        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
      </options>
    </param>
  </when>
  <when value="history">
    <param name="own_file" type="data" format="fasta" label="Select reference genome" />
  </when>
</conditional>

The Bowtie 2 wrapper also demonstrates other conditional paths - such as choosing between paired inputs of single stranded inputs.

Attributes

Attribute	Details	Required
name	Name for this element	False
value_from	Infrequently used option to dynamically access Galaxy internals, this should be avoided. Galaxy method to execute.	False
value_ref	Infrequently used option to dynamically access Galaxy internals, this should be avoided. Referenced parameter to pass method.	False
``value_ref_in_group` `	Infrequently used option to dynamically access Galaxy internals, this should be avoided. Is referenced parameter is the same group.	False
label	Human readable description for the conditional, unused in the Galaxy UI currently.	False

tool > inputs > conditional > when

This directive describes one potential set of input for the tool at this depth. See documentation for the conditional block for more details and examples (XML and corresponding Cheetah conditionals).

Attributes

Attribute	Details	Required
value	Value for the tool form test parameter corresponding to this when block.	True

tool > inputs > param

Contained within the <inputs> tag set - each of these specifies a field that will be displayed on the tool form. Ultimately, the values of these form fields will be passed as the command line parameters to the tool’s executable.

Common Attributes

The attributes valid for this tag vary wildly based on the type of the parameter being described. All the attributes for the param element are documented below for completeness, but here are the common ones for each type are as follows:

Attributes

Attribute	Details	Required
type	Describes the parameter type - each different type as different semantics and the tool form widget is different. Currently valid parameter types are: text, integer, float, boolean, genomebuild, select, color, data_column, hidden, hidden_data, baseurl, file, ftpfile, data, data_collection, library_data, drill_down. The definition of supported parameter types as defined in the parameter_types dictionary in /lib/galaxy/tools/pa rameters/basic.py.	True
name	Name for this element. This name is used as the Cheetah variable containing the user-supplied parameter name in command and configfile elements. The name should not contain pipes or periods (e.g. .). Some “reserved” names are REDIRECT_URL, DATA_URL, GALAXY_URL.	False
argument	If the parameter reflects just one command line argument of a certain tool, this tag should be set to that particular argument. It is rendered in parenthesis after the help section, and it will create the name attribute from the argument attribute by stripping the dashes (e.g. if argument="--sensiti ve" then name="sensitive" is implicit).	False
label	The attribute value will be displayed on the tool page as the label of the form field (``label=”Sort Query” ``).	False
help	Short bit of text, rendered on the tool form just below the associated field to provide information about the field. Find the Intergalactic Utilities Commision suggested best practices for this element here.	False
optional	If false, parameter must have a value. Defaults to “false”.	False
refresh_on_change	Force a reload of the tool panel when the value of this parameter changes to allow code file processing. See deprecation-like notice for code blocks.	False

Parameter Types

text

When type="text", the parameter is free form text and appears as a text box in the tool form.

Examples

Sometimes you need labels for data or graph axes, chart titles, etc. This can be done using a text field. The following will create a text box 30 characters wide with the default value of “V1”.

<param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>

The size parameter can be two dimensional, if it is the textbox will be rendered on the tool form as a text area instead of a single line text box.

<param name="foo" type="text" area="true" size="5x25" />

As of 17.01, text parameters can also supply a static list of preset defaults options. The user may be presented with the option to select one of these but will be allowed to supply an arbitrary text value.

<param name="foo" type="text" value="foo 1">
    <option value="foo 1">Foo 1 Display</option>
    <option value="foo 2">Foo 2 Display</option>
</param>

See param_text_option.xml for a demonstration of this.

Attributes

Attribute	Details	Required
area	Boolean indicating if this should be rendered as a one line text box (if false) or a multi-line text area (if true).	False
value	The default value for this parameter.	False
size	Used only if type attribute value is text. To create a multi-line text box add an area="true" attribute to the param tag. This can be one dimensional (e.g. size="40") or two dimensional (e.g. size="5x25").	False

integer and float

These parameters represent whole number and real numbers, respectively.

Example

<param name="region_size" size="4" type="integer" value="1" label="flanking regions of size" />

Attributes

Attribute	Details	Required
value	The default value for this parameter.	False
min	Minimum valid parameter value - only valid when type is integer or float.	False
max	Maximum valid parameter value - only valid when type is integer or float.	False

boolean

This represents a binary true or false value.

Attributes

Attribute	Details	Required
checked	Set to true if the boolean parameter should be checked (or true) by default.	False
truevalue	The parameter value in the Cheetah template if the parameter is true or checked by the user. Only valid if type is boolean.	False
falsevalue	The parameter value in the Cheetah template if the parameter is false or not checked by the user. Only valid if type is boolean.	False

data

A dataset from the current history. Multiple types might be used for the param form.

Examples

The following will find all “coordinate interval files” contained within the current history and dynamically populate a select list with them. If they are selected, their destination and internal file name will be passed to the appropriate command line variable.

<param name="interval_file" type="data" format="interval" label="near intervals in"/>

The following demonstrates a param which may accept multiple files and multiple formats.

<param format="sam,bam" multiple="true" name="bamOrSamFile" type="data"
       label="Alignments in BAM or SAM format"
       help="The set of aligned reads." />

Perhaps counter-intuitively, a multiple="true" data parameter requires at least one data input. If optional="true" is specified, this condition is relaxed and the user is allowed to select 0 datasets. Unfortunately, if 0 datasets are selected the resulting value for the parameter during Cheetah templating (such as in a command block) will effectively be a list with one None-like entity in it.

The following idiom can be used to iterate over such a list and build a hypothetical -B parameter for each file - the if block is used to handle the case where a None-like entity appears in the list because no files were selected:

#for $input in $input1
    #if $input
        -B "$input"
    #end if
#end for

Some example tools using multiple="true" data parameters include:

• multi_data_param.xml
• multi_data_optional.xml

Additionally, a detailed discussion of handling multiple homogenous files can be found in the the Planemo Documentation on this topic.

Attributes

Attribute	Details	Required
format	Only if type attribute value is data or data_collection - the list of supported data formats is contained in the /config/datatypes_co nf.xml.sample file. Use the file extension.	False
multiple	Allow multiple valus to be selected. Valid with data and select parameters.	False

select

The following will create a select list containing the options “Downstream” and “Upstream”. Depending on the selection, a d or u value will be passed to the $upstream_or_down variable on the command line.

<param name="upstream_or_down" type="select" label="Get">
  <option value="u">Upstream</option>
  <option value="d">Downstream</option>
</param>

The following will create a checkbox list allowing the user to select “Downstream”, “Upstream”, both, or neither. Depending on the selection, the value of $upstream_or_down will be d, u, u,d, or “”.

<param name="upstream_or_down" type="select" label="Get" multiple="true" display="checkboxes">
  <option value="u">Upstream</option>
  <option value="d">Downstream</option>
</param>

Attributes

Attribute	Details	Required
data_ref	Only valid if type attribute value is select or data_column. Used with select lists whose options are dynamically generated based on certain metadata attributes of the dataset upon which this parameter depends (usually but not always the tool’s input dataset).	False
display	This attribute is used only if type attribute value is select - render a select list as a set of check boxes or radio buttons. Defaults to a drop-down menu select list.	False
multiple	Allow multiple valus to be selected. Valid with data and select parameters.	False
dynamic_options	Deprecated/discourage d method to allow access to Python code to generate options for a select list. See code’s documentation for an example.	False

data_column

This parameter type is used to select columns from a parameter.

Attributes

Attribute	Details	Required
force_select	Used only if the type attribute value is data_column, this is deprecated and the inverse of optional. Set to false to not force user to select an option in the list.	False
numerical	Used only if the type attribute value is data_column, if true the column will be treated as numerical when filtering columns based on metadata.	False

drill_down

Attributes

Attribute	Details	Required
hierarchy	Used only if the type attribute value is drill_down, this attribute determines the drill down is recursive or exact.	False

data_collection

The following will create a parameter that only accepts paired FASTQ files grouped into a collection.

Examples

<param name="inputs" type="data_collection" collection_type="paired" label="Input FASTQs" format="fastq">
</param>

More detailed information on writing tools that consume collections can be found in the planemo documentation.

Attributes

Attribute	Details	Required
format	Only if type attribute value is data or data_collection - the list of supported data formats is contained in the /config/datatypes_co nf.xml.sample file. Use the file extension.	False
collection_type	This is only valid if type is data_collection. Restrict the kind of collection that can be consumed by this parameter (e.g. paired, list:paired, list). Multiple such collection types can be specified here as a comma separated list.	False

color

Examples

The following example will create a color selector parameter.

<param name="feature_color" type="color" label="Default feature color" value="#ff00ff">
</param>

Given that the output includes a pound sign, it is often convenient to use a sanitizer to prevent Galaxy from escaping the result.

<param name="feature_color" type="color" label="Default feature color" value="#ff00ff">
  <sanitizer>
    <valid initial="string.letters,string.digits">
      <add value="#" />
    </valid>
  </sanitizer>
</param>

Attributes

Attribute	Details	Required
value	The default value for this parameter.	False
rgb	If false, the returned value will be in Hex color code. If true it will be a RGB value e.g. 0,0,255. This attribute is only valid when type is color.	False

This covers examples of the most common parameter types, the remaining parameter types are more obsecure and less likely to be useful for most tool authors.

Attributes

Attribute	Details	Required
type	Describes the parameter type - each different type as different semantics and the tool form widget is different. Currently valid parameter types are: text, integer, float, boolean, genomebuild, select, color, data_column, hidden, hidden_data, baseurl, file, ftpfile, data, data_collection, library_data, drill_down. The definition of supported parameter types as defined in the parameter_types dictionary in /lib/galaxy/tools/pa rameters/basic.py.	True
name	Name for this element. This name is used as the Cheetah variable containing the user-supplied parameter name in command and configfile elements. The name should not contain pipes or periods (e.g. .). Some “reserved” names are REDIRECT_URL, DATA_URL, GALAXY_URL.	False
area	Boolean indicating if this should be rendered as a one line text box (if false) or a multi-line text area (if true).	False
argument	If the parameter reflects just one command line argument of a certain tool, this tag should be set to that particular argument. It is rendered in parenthesis after the help section, and it will create the name attribute from the argument attribute by stripping the dashes (e.g. if argument="--sensiti ve" then name="sensitive" is implicit).	False
label	The attribute value will be displayed on the tool page as the label of the form field (``label=”Sort Query” ``).	False
help	Short bit of text, rendered on the tool form just below the associated field to provide information about the field. Find the Intergalactic Utilities Commision suggested best practices for this element here.	False
value	The default value for this parameter.	False
default_value	Deprecated way to specify default value for column parameters (use value instead).	False
optional	If false, parameter must have a value. Defaults to “false”.	False
rgb	If false, the returned value will be in Hex color code. If true it will be a RGB value e.g. 0,0,255. This attribute is only valid when type is color.	False
min	Minimum valid parameter value - only valid when type is integer or float.	False
max	Maximum valid parameter value - only valid when type is integer or float.	False
format	Only if type attribute value is data or data_collection - the list of supported data formats is contained in the /config/datatypes_co nf.xml.sample file. Use the file extension.	False
collection_type	This is only valid if type is data_collection. Restrict the kind of collection that can be consumed by this parameter (e.g. paired, list:paired, list). Multiple such collection types can be specified here as a comma separated list.	False
data_ref	Only valid if type attribute value is select or data_column. Used with select lists whose options are dynamically generated based on certain metadata attributes of the dataset upon which this parameter depends (usually but not always the tool’s input dataset).	False
accept_default	Documentation for PermissiveBoolean	False
refresh_on_change	Force a reload of the tool panel when the value of this parameter changes to allow code file processing. See deprecation-like notice for code blocks.	False
force_select	Used only if the type attribute value is data_column, this is deprecated and the inverse of optional. Set to false to not force user to select an option in the list.	False
use_header_names	Used only if the type attribute value is data_column, if true Galaxy assumes first row of data_ref is a header and builds the select list with these values rather than the more generic c1 … cN.	False
display	This attribute is used only if type attribute value is select - render a select list as a set of check boxes or radio buttons. Defaults to a drop-down menu select list.	False
multiple	Allow multiple valus to be selected. Valid with data and select parameters.	False
numerical	Used only if the type attribute value is data_column, if true the column will be treated as numerical when filtering columns based on metadata.	False
hierarchy	Used only if the type attribute value is drill_down, this attribute determines the drill down is recursive or exact.	False
checked	Set to true if the boolean parameter should be checked (or true) by default.	False
truevalue	The parameter value in the Cheetah template if the parameter is true or checked by the user. Only valid if type is boolean.	False
falsevalue	The parameter value in the Cheetah template if the parameter is false or not checked by the user. Only valid if type is boolean.	False
size	Used only if type attribute value is text. To create a multi-line text box add an area="true" attribute to the param tag. This can be one dimensional (e.g. size="40") or two dimensional (e.g. size="5x25").	False
dynamic_options	Deprecated/discourage d method to allow access to Python code to generate options for a select list. See code’s documentation for an example.	False

tool > inputs > param > validator

See the annotation_profiler tool for an example of how to use this tag set. This tag set is contained within the tag set - it applies a validator to the containing parameter.

Examples

The following demonstrates a simple validator unspecified_build ensuring that a dbkey is present on the selected dataset. This example is taken from the extract_genomic_dna tool.

<param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
    <validator type="unspecified_build" />
</param>

Along the same line, the following example taken from samtools_mpileup ensures that a dbkey is present and that FASTA indices in the fasta_indexes tool data table are present.

<param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="true">
    <validator type="unspecified_build" />
    <validator type="dataset_metadata_in_data_table" metadata_name="dbkey" table_name="fasta_indexes" metadata_column="1"
               message="Sequences are not currently available for the specified build." />
</param>

In this older, somewhat deprecated example - a genome build of the dataset must be stored in Galaxy clusters and the name of the genome (dbkey) must be one of the values in the first column of file alignseq.loc - that could be expressed with the validator. In general, dataset_metadata_in_file should be considered deprecated in favor of

<validator type="dataset_metadata_in_file"
           filename="alignseq.loc"
           metadata_name="dbkey"
           metadata_column="1"
           message="Sequences are not currently available for the specified build."
           split=" "
           line_startswith="seq" />

A very common validator is simply ensure a Python expression is valid for a specified value. In the following example - paths/names that downstream tools use in filenames may not contain ...

<validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>

Attributes

Attribute	Details	Required
type	The list of supported validators is in the validator_types dictionary in /lib/galaxy/tools/pa rameters/validation.p y. Valid values include: expression, regex, in_range, length, metadata, unspecified_build , no_options, empty_field, dataset_metadata_in _file, dataset_metadata_in _data_table, dataset_ok_validato r	True
message	The error message displayed on the tool form if validation fails.	False
check	Comma-seperated list of metadata fields to check for if type is metadata. If not specified, all non-optional metadata fields will be checked unless they appear in the list of fields specified by the skip attribute.	False
table_name	Tool data table name to check against if type is dataset_metadata_in _tool_data. See the documentation for tool data tables and `data managers <https://gal axyproject.org/admin/ tools/data-managers/> `__ for more information.	False
filename	Tool data filename to check against if type is dataset_metadata_in _file. File should be present Galaxy’s tool-data directory.	False
metadata_name	Target metadata attribute name for dataset_metadata_in _data_table and dataset_metadata_in _file options.	False
metadata_column	Target column for metadata attribute in dataset_metadata_in _data_table and dataset_metadata_in _file options. This can be an integer index to the column or a column name.	False
line_startswith	Used to indicate lines in the file being used for validation start with a this attribute value.	False
min	When the type attribute value is in_range - this is the minimum number allowed.	False
max	When the type attribute value is in_range - this is the maximum number allowed.	False
exclude_min	When the type attribute value is in_range - this boolean indicates if the min value is allowed.	False
exclude_max	When the type attribute value is in_range - this boolean indicates if the max value is allowed.	False
split	If type is `dataset_metadata_in _file``, this attri bute is the column se parator to use for va lues in the specified file. This default i s``\tand due to a bug in older versio ns of Galaxy, should not be modified. | Fa lseskip| Comm a-seperated list of m etadata fields to ski p if type ismetad ata. If not speci fied, all non-optiona l metadata fields wil l be checked unless check`` attribute is specified.	False

tool > inputs > param > option

See /tools/filters/sorter.xml for typical examples of how to use this tag set. This directive is used to described static lists of options and is contained within the param directive when the type attribute value is select (i.e. <param type="select" ...>).

Example

<param name="style" type="select" label="with flavor">
    <option value="num">Numerical sort</option>
    <option value="gennum">General numeric sort</option>
    <option value="alpha">Alphabetical sort</option>
</param>

An option can also be annotated with selected="true" to specify a default option.

<param name="col" type="select" label="From">
    <option value="0" selected="true">Column 1 / Sequence name</option>
    <option value="1">Column 2 / Source</option>
    <option value="2">Column 3 / Feature</option>
    <option value="6">Column 7 / Strand</option>
    <option value="7">Column 8 / Frame</option>
</param>

Attributes

Attribute	Details	Required
value	The value of the corresponding variable when used the Cheetah template. Also the value that should be used in building test cases and used when building requests for the API.	False
selected	A boolean parameter indicating if the corresponding option is selected by default (the default is false).	False

tool > inputs > param > conversion

A contrived example of a tool that uses this is the test tool explicit_conversion.xml.

This directive is optionally contained within the <param> tag when the type attribute value is data and is used to dynamically generated a converted dataset for the contained input of the type specified using the type tag.

Attributes

Attribute	Details	Required
name	Name of Cheetah variable to create for converted dataset.	True
type	The short extension describing the datatype to convert to - Galaxy must have a datatype converter from the parent input’s type to this.	True

tool > inputs > param > options

See /tools/extract/liftOver_wrapper.xml for an example of how to use this tag set. This tag set is optionally contained within the <param> tag when the type attribute value is select or data and used to dynamically generated lists of options. This tag set dynamically creates a list of options whose values can be obtained from a predefined file stored locally or a dataset selected from the current history.

There are at least five basic ways to use this tag - four of these correspond to a from_XXX attribute on the options directive and the other is to exclusively use filters to populate options.

• from_data_table - The options for the select list are dynamically obtained from a file specified in the Galaxy configuration file tool_data_table_conf.xml or from a Tool Shed installed data manager.
• from_dataset - The options for the select list are dynamically obtained from input dataset selected for the tool from the current history.
• from_file - The options for the select list are dynamically obtained from a file. This mechanis is discourage in favor of the more generic from_data_table.
• from_parameter - The options for the select list are dynamically obtained from a parameter.
• Using filters - various filters can be used to populate options, see examples in the filter documentation.

from_data_table

See Galaxy’s data tables documentation for information on setting up data tables.

Once a data table has been configured and populated, these can be easily leveraged via tools.

This conditional block in the bowtie2 wrapper demonstrates using from_data_table options as an alternative to local reference data.

<conditional name="reference_genome">
  <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
    <option value="indexed">Use a built-in genome index</option>
    <option value="history">Use a genome from the history and build index</option>
  </param>
  <when value="indexed">
    <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
      <options from_data_table="bowtie2_indexes">
        <filter type="sort_by" column="2"/>
        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
      </options>
    </param>
  </when>
  <when value="history">
    <param name="own_file" type="data" format="fasta" label="Select reference genome" />
  </when>
</conditional>

A minimal example wouldn’t even need the filter or validator above, but they are frequently nice features to add to your wrapper and can improve the user experience of a tool.

from_dataset

The following example is taken from the Mothur tool remove.lineage.xml and demonstrates generating options from a dataset directly.

<param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy" help="please make sure your file has no quotation marks in it"/>
<param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
    <options from_dataset="taxonomy">
        <column name="name" index="1"/>
        <column name="value" index="1"/>
        <filter type="unique_value" name="unique_taxon" column="1"/>
        <filter type="sort_by" name="sorted_taxon" column="1"/>
    </options>
    <sanitizer>
        <valid initial="default">
            <add preset="string.printable"/>
            <add value=";"/>
            <remove value="&quot;"/>
            <remove value="&apos;"/>
        </valid>
    </sanitizer>
</param>

Filters can be used to generate options from dataset directly also as the example below demonstrates (many more examples are present in the filter documentation).

<param name="species1" type="select" label="When Species" multiple="false">
    <options>
        <filter type="data_meta" ref="input1" key="species" />
    </options>
</param>

from_file

The following example is for Blast databases. In this example users maybe select a database that is pre-formatted and cached in Galaxy clusters. When a new dataset is available, admins must add the database to the local file named “blastdb.loc”. All such databases in that file are included in the options of the select list. For a local instance, the file (e.g. blastdb.loc or alignseq.loc) must be stored in the configured tool_data_path directory. In this example, the option names and values are taken from column 0 of the file.

<param name="source_select" type="select" display="radio" label="Choose target database">
    <options from_file="blastdb.loc">
        <column name="name" index="0"/>
        <column name="value" index="0"/>
    </options>
</param>

In general, from_file should be considered deprecated and from_data_table should be prefered.

from_parameter

This variant of the options directive is discouraged because it exposes internal Galaxy structures. See the older bowtie wrappers for an example of these.

Other Ways to Dynamically Generate Options

Though deprecated and discouraged, code blocks can also be used to generate dynamic options.

Attributes

Attribute	Details	Required
from_dataset	Documentation for from_dataset	False
from_file	Documentation for from_file	False
from_data_table	Documentation for from_data_table	False
from_parameter	Documentation for from_parameter	False
options_filter_attr ibute	Documentation for options_filter_attrib ute	False
transform_lines	Documentation for transform_lines	False
startswith	Documentation for startswith	False

tool > inputs > param > options > column

Optionally contained within an <options> tag set - specifies columns used in building select options from a file stored locally (i.e. index or tool data) or a dataset in the current history.

Any number of columns may be described, but at least one must be given the name value and it will serve as the value of this parameter in the Cheetah template and elsewhwere (e.g. in API for instance).

If a column named name is defined, this too has special meaning and it will be the value the tool form user sees for each option. If no name column appears, value will serve as the name.

Examples

The following fragment shows options from the dataset in the current history that has been selected as the value of the parameter named input1.

<options from_dataset="input1">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
</options>

The interval2maf tool makes use of this tag with files from a history, and the star_fusion tool makes use of this to reference a data table.

Attributes

Attribute	Details	Required
name	Name given to the column with index index, the names name and value have special meaning as described above.	True
index	0-based index of the column in the target file.	True

tool > inputs > param > options > filter

Optionally contained within an <options> tag set - filter out values obtained from a locally stored file (e.g. a tool data table) or a dataset in the current history.

Examples

The following example from Mothur’s remove.groups.xml tool demonstrates filtering a select list based on the metadata of an input to to the tool.

<param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
<param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
    <options>
        <filter type="data_meta" ref="group_in" key="groups"/>
    </options>
</param>

This more advanced example, taken from Mothur’s remove.lineage.xml tool demonstrates using filters to sort a list and remove duplicate entries.

<param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file" help="please make sure your file has no quotation marks in it"/>
<param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
    <options from_dataset="taxonomy">
        <column name="name" index="2"/>
        <column name="value" index="2"/>
        <filter type="unique_value" name="unique_taxon" column="2"/>
        <filter type="sort_by" name="sorted_taxon" column="2"/>
    </options>
    <sanitizer>
        <valid initial="default">
            <add preset="string.printable"/>
            <add value=";"/>
            <remove value="&quot;"/>
            <remove value="&apos;"/>
        </valid>
    </sanitizer>
</param>

This example taken from the hisat2 tool demonstrates filtering values from a tool data table.

<param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select">
    <options from_data_table="hisat2_indexes">
        <filter column="2" type="sort_by" />
        <validator message="No genomes are available for the selected input dataset" type="no_options" />
    </options>
</param>

The gemini_load.xml tool demonstrates adding values to an option list using filters.

<param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">
    <options>
        <filter type="add_value" value="hg19" />
        <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
        <filter type="add_value" value="hg_g1k_v37" />
    </options>
</param>

While this fragment from maf_to_interval.xml demonstrates removing items.

<param name="species" type="select" label="Select additional species"
       display="checkboxes" multiple="true"
       help="The species matching the dbkey of the alignment is always included.
       A separate history item will be created for each species.">
    <options>
        <filter type="data_meta" ref="input1" key="species" />
        <filter type="remove_value" meta_ref="input1" key="dbkey" />
    </options>
</param>

This example taken from snpSift_dbnsfp.xml demonstrates splitting up strings into multiple values.

<param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
    <options from_data_table="snpsift_dbnsfps">
        <column name="name" index="4"/>
        <column name="value" index="4"/>
        <filter type="param_value" ref="dbnsfp" column="3" />
        <filter type="multiple_splitter" column="4" separator=","/>
    </options>
</param>

Attributes

Attribute	Details	Required
type	These values are defined in the module /lib/galaxy/tools/pa rameters/dynamic_opti ons.py in the filter_types dictionary. Currently defined values are: data_meta, param_value, static_value, unique_value, multiple_splitter , attribute_value_spl itter, add_value, remove_value, and sort_by	True
column	Column targeted by this filter - this attribute is unused and invalid if type is add_value or remove_value. This can be a column index or a column name.	False
name	Name displayed for value to add (only used with type of add_value).	False
ref	The attribute name of the reference file (tool data) or input dataset. Only used when type is data_meta (required), param_value (required), or remove_value (optional).	False
key	When type is data_meta, param_value, or remove_value - this is the name of the metadata key to filter by.	False
multiple	For types data_meta and remove_value, whether option values are multiple. Columns will be split by separator. Defaults to false.	False
separator	When type is data_meta, multiple_splitter , or remove_value - this is used to split one value into multiple parts. When type is data_meta or remove_value this is only used if multiple is set to true.	False
keep	If true, keep columns matching the value, if false discard columns matching the value. Used when type is either static_value or param_value.	False
value	Target value of the operations - has slightly different meanings depending on type. For instance when type is add_value it is the value to add to the list and when type is static_value it is the value compared against.	False
ref_attribute	Only used when type is param_value. Period (.) separated attribute chain of input (ref) attributes to use as value for filter.	False
index	Used when type is add_value, it is the index into the list to add the option to. If not set, the option will be added to the end of the list.	False
meta_ref	Only used when type is remove_value. Dataset to look for the value of metadata key to remove from the list.	False

tool > inputs > param > sanitizer

See /tools/filters/grep.xml for a typical example of how to use this tag set. This tag set is used to replace the basic parameter sanitization with custom directives. This tag set is contained within the <param> tag set - it contains a set of <valid> and <mapping> tags.

Examples

This example replaces the invalid character default of X with the empty string (so invalid characters are effectively dropped instead of replaced with X) and indicates the only valid characters for this input are ASCII letters, ASCII digits, and _.

<param name="mystring" type="text" label="Say something interesting">
    <sanitizer invalid_char="">
        <valid initial="string.letters,string.digits"><add value="_" /> </valid>
    </sanitizer>
</param>

This example allows many more valid characters and specifies that & will just be dropped from the input.

<sanitizer>
    <valid initial="string.printable">
        <remove value="&apos;"/>
    </valid>
    <mapping initial="none">
        <add source="&apos;" target=""/>
    </mapping>
</sanitizer>

Attributes

Attribute	Details	Required
sanitize	This boolean parameter determines if the input is sanitized at all (the default is true).	False
invalid_char	The attribute specifies the character used as a replacement for invalid characters.	False

tool > inputs > param > sanitizer > valid

Contained within the <sanitizer> tag set, these are used to specify a list of allowed characters. Contains <add> and <remove> tags.

Attributes

Attribute	Details	Required
initial	This describes the initial characters to allow as valid, the default is string.letters + st ring.digits + " -=_.( )/+*^,:?!"	False

tool > inputs > param > sanitizer > valid > add

This directive is used to add individual characters or preset lists of characters. Character must not be allowed as a valid input for the mapping to occur. Preset lists include default and none as well as those available from string.* (e.g. string.printable).

Attributes

Attribute	Details	Required
preset	Add target characters from the list of valid characters (e.g. string.printable) .	False
value	Add a character to the list of valid characters.	False

tool > inputs > param > sanitizer > valid > remove

This directive is used to remove individual characters or preset lists of characters. Character must not be allowed as a valid input for the mapping to occur. Preset lists include default and none as well as those available from string.* (e.g. string.printable).

Attributes

Attribute	Details	Required
preset	Remove characters from the list of valid characters (e.g. string.printable) .	False
value	A character to remove from the list of valid characters.	False

tool > inputs > param > sanitizer > mapping

Contained within the tag set. Used to specify a mapping of disallowed character to replacement string. Contains and tags.

Attributes

Attribute	Details	Required
initial	initial character mapping (default is galaxy.util.mapped_ chars)	False

tool > inputs > param > sanitizer > mapping > add

Use to add character mapping during sanitization. Character must not be allowed as a valid input for the mapping to occur.

Attributes

Attribute	Details	Required
source	Replace all occurrences of this character with the string of target.	False
target	Replace all occurrences of source with this string	False

tool > inputs > param > sanitizer > mapping > remove

Use to remove character mapping during sanitization.

Attributes

Attribute	Details	Required
source	Character to remove from mapping.	False

tool > request_param_translation

See /tools/data_source/ucsc_tablebrowser.xml for an example of how to use this tag set. This tag set is used only in “data_source” tools (i.e. whose tool_type attribute is data_source). This tag set contains a set of request_param elements.

tool > request_param_translation > request_param

Contained within the request_param_translation tag set (used only in “data_source” tools). The external data source application may send back parameter names like “GENOME” which must be translated to “dbkey” in Galaxy.

Attributes

Attribute	Details	Required
galaxy_name	Each of these maps directly to a remote_name value	True
remote_name	The string representing the name of the parameter in the remote data source	True
missing	The default value to use for galaxy_name if the remote_name parameter is not included in the request	False

tool > request_param_translation > request_param > append_param

Optionally contained within the request_param element if galaxy_name="URL". Some remote data sources (e.g., Gbrowse, Biomart) send parameters back to Galaxy in the initial response that must be added to the value of “URL” prior to Galaxy sending the secondary request to the remote data source via URL.

Attributes

Attribute	Details	Required
separator	The text to use to join the requested parameters together (example separator="&" ).	True
first_separator	The text to use to join the request_param parameters to the first requested parameter (example ``first_separator=”?” ``).	False
join	The text to use to join the param name to its value (example join="=").	True

tool > request_param_translation > request_param > append_param > value

Contained within the append_param tag set. Allows for appending a param name / value pair to the value of URL.

Example:

<request_param_translation>
    <request_param galaxy_name="URL" remote_name="URL" missing="">
        <append_param separator="&amp;" first_separator="?" join="=">
            <value name="_export" missing="1" />
        </append_param>
    </request_param>
</request_param_tranlsation>

Attributes

Attribute	Details	Required
name	Any valid HTTP request parameter name. The name / value pair must be received from the remote data source and will be appended to the value of URL as something like "&_export=1" (e.g. name="_export").	True
missing	Must be a valid HTTP request parameter value (e.g. missing="1").	True

tool > request_param_translation > request_param > value_translation

Optionally contained within the request_param tag set. The parameter value received from a remote data source may be named differently in Galaxy, and this tag set allows for the value to be appropriately translated.

tool > request_param_translation > request_param > value_translation > value

Contained within the value_translation tag set - allows for changing the data type value to something supported by Galaxy.

Example:

<request_param_translation>
    <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
        <value_translation>
            <value galaxy_value="tabular" remote_value="primaryTable" />
        </value_translation>
    </request_param>
</request_param_tranlsation>

Attributes

Attribute	Details	Required
galaxy_value	The target value (e.g. for setting data format: the list of supported data formats is contained in the /config/datatypes_co nf.xml.sample.	True
remote_value	The value supplied by the remote data source application	True

tool > outputs

Container tag set for the <data> and <collection> tag sets. The files and collections created by tools as a result of their execution are named by Galaxy. You specify the number and type of your output files using the contained <data> and <collection> tags. These may be passed to your tool executable through using line variables just like the parameters described in the <inputs> documentation.

Attributes

Attribute	Details	Required
provided_metadata_s tyle	Style used for tool provided metadata file (i.e. galaxy.json) - this can be either “legacy” or “default”. The default of tools with a profile of 17.09 or newer are “default”, and “legacy” for older and tools and tools without a specified profile. A discussion of the differences between the styles can be found at https://github.com/ga laxyproject/galaxy/pu ll/4437.	False
provided_metadata_f ile	Path relative to tool’s working directory to load tool provided metadata from. This metadata can describe dynamic datasets to load, dynamic collection contents, as well as simple metadata (e.g. name, dbkey, etc…) and datatype specific metadata for declared outputs. More information can be found here. The default is galaxy.json.	False

tool > outputs > data

This tag set is contained within the <outputs> tag set, and it defines the output data description for the files resulting from the tool’s execution. The value of the attribute label can be acquired from input parameters or metadata in the same way that the command line parameters are (discussed in the tag set section above).

Examples

The following will create a variable called $out_file1 with data type pdf.

<outputs>
    <data format="pdf" name="out_file1" />
</outputs>

The valid values for format can be found in /config/datatypes_conf.xml.sample.

The following will create a dataset in the history panel whose data type is the same as that of the input dataset selected (and named input1) for the tool.

<outputs>
    <data format_source="input1" name="out_file1" metadata_source="input1"/>
</outputs>

The following will create datasets in the history panel, setting the output data type to be the same as that of an input dataset named by the format_source attribute. Note that a conditional name is not included, so 2 separate conditional blocks should not contain parameters with the same name.

<inputs>
    <!-- fasta may be an aligned fasta that subclasses Fasta -->
    <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
    <conditional name="qual">
        <param name="add" type="select" label="Trim based on a quality file?" help="">
            <option value="no">no</option>
            <option value="yes">yes</option>
        </param>
        <when value="no"/>
        <when value="yes">
            <!-- qual454, qualsolid, qualillumina -->
            <param name="qfile" type="data" format="qual" label="qfile - a quality file"/>
        </when>
    </conditional>
</inputs>
<outputs>
    <data format_source="fasta" name="trim_fasta"
          label="${tool.name} on ${on_string}: trim.fasta"/>
    <data format_source="qfile" name="trim_qual"
          label="${tool.name} on ${on_string}: trim.qual">
        <filter>qual['add'] == 'yes'</filter>
    </data>
</outputs>

Assume that the tool includes an input parameter named database which is a select list (as shown below). Also assume that the user selects the first option in the $database select list. Then the following will ensure that the tool produces a tabular data set whose associated history item has the label Blat on Human (hg18).

<inputs>
    <param format="tabular" name="input" type="data" label="Input stuff"/>
    <param type="select" name="database" label="Database">
        <option value="hg18">Human (hg18)</option>
        <option value="dm3">Fly (dm3)</option>
    </param>
</inputs>
<outputs>
    <data format="input" name="output" label="Blat on ${database.value_label}" />
</outputs>

Attributes

Attribute	Details	Required
name	Name for this output. This name is used as the Cheetah variable containing the Galaxy assigned output path in command and configfile elements. The name should not contain pipes or periods (e.g. .).	False
auto_format	If true, this output will sniffed and its format determined automatically by Galaxy.	False
format	The short name for the output datatype. The valid values for format can be found in /config/datatypes_co nf.xml.sample (e.g. format="pdf" or format="fastqsanger ").	False
format_source	This sets the data type of the output file to be the same format as that of a tool input dataset.	False
default_identifier_ source	Sets the source of element identifier to the specified input. This only applies to collections that are mapped over a non-collection input and that have equivalent structures. If this references input elements in conditionals, this value should be qualified (e.g. cond|input instead of input if input is in a conditional with name="cond").	False
metadata_source	This copies the metadata information from the tool’s input dataset. This is particularly useful for interval data types where the order of the columns is not set.	False
label	This will be the name of the history item for the output data set. The string can include structure like ${<some param name> .<some attribute>}, as discussed for command line parameters in the <command> tag set section above. The default label is ${tool.name} on ${o n_string}.	False
from_work_dir	Relative path to a file produced by the tool in its working directory. Output’s contents are set to this file’s contents.	False
hidden	Boolean indicating whether to hide dataset in the history view. (Default is false.)	False

tool > outputs > data > filter

The <data> tag can contain a <filter> tag which includes a Python code block to be executed to test whether to include this output in the outputs the tool ultimately creates. If the code, when executed, returns True, the output dataset is retained. In these code blocks the tool parameters appear as Python variables and are thus referred to without the $ used for the Cheetah template (used in the <command> tag). Variables that are part of conditionals are accessed using a hash named after the conditional.

Example

<inputs>
  <param type="data" format="fasta" name="reference_genome" label="Reference genome" />
  <param type="data" format="bam" name="input_bam" label="Aligned reads" />
  <conditional name="options">
    <param label="Use advanced options" name="selection_mode" type="select">
      <option selected="true" value="defaults">Use default options</option>
      <option value="advanced">Use advanced options</option>
    </param>
    <when value="defaults"> </when>
    <when value="advanced">
      <param name="vcf_output" type="boolean" checked="false" label="VCF output"
        truevalue="--vcf" falsevalue="" />
    </when>
  <conditional>
</inputs>
<outputs>
  <data format="txt" label="Alignment report on ${on_string}" name="output_txt" />
  <data format="vcf" label="Variant summary on ${on_string}" name="output_vcf">
      <filter>options['selection_mode'] == 'advanced' and options['vcf_output']</filter>
  </data>
</outputs>

tool > outputs > data > change_format

See extract_genomic_dna.xml or the test tool output_format.xml for simple examples of how this tag set is used in a tool. This tag set is optionally contained within the <data> tag set and is the container tag set for the following <when> tag set.

tool > outputs > data > change_format > when

If the data type of the output dataset is the specified type, the data type is changed to the desired type.

Examples

Assume that your tool config includes the following select list parameter structure:

<param name="out_format" type="select" label="Output data type">
    <option value="fasta">FASTA</option>
    <option value="interval">Interval</option>
</param>

Then whenever the user selects the interval option from the select list, the following structure in your tool config will override the format="fasta" setting in the <data> tag set with format="interval".

<outputs>
    <data format="fasta" name="out_file1">
        <change_format>
            <when input="out_format" value="interval" format="interval" />
        </change_format>
    </data>
</outputs>

See extract_genomic_dna.xml or the test tool output_format.xml for more examples.

Attributes

Attribute	Details	Required
input	This attribute should be the name of the desired input parameter (e.g. ``input=”out_format”` ` above).	False
value	This must be a possible value of the input parameter (e.g. value="interval" above), or of the deprecated input_dataset’s attribute.	True
format	This value must be a supported data type (e.g. format="interval" ). See /config/datatypes_co nf.xml.sample for a list of supported formats.	True
input_dataset	Deprecated.	False
attribute	Deprecated.	False

tool > outputs > data > actions

The actions directive allows tools to dynamically take actions related to an output either unconditionally or conditionally based on inputs. These actions currently include setting metadata values and the output’s data format.

The examples below will demonstrate that the actions tag contains child conditional tags. The these conditionals are met, additional action directives below the conditional are apply to the data output.

Metadata

The <actions> in the Bowtie 2 wrapper is used in lieu of the deprecated <code> tag to set the dbkey of the output dataset. In bowtie2_wrapper.xml (see below), according to the first action block, if the `reference_genome.source is indexed (not history), then it will assign the dbkey of the output file to be the same as that of the reference file. It does this by looking at through the data table and finding the entry that has the value that’s been selected in the index dropdown box as column 1 of the loc file entry and using the dbkey, in column 0 (ignoring comment lines (starting with #) along the way).

If reference_genome.source is history, it pulls the dbkey from the supplied file.

<data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
  <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
  <actions>
    <conditional name="reference_genome.source">
      <when value="indexed">
        <action type="metadata" name="dbkey">
          <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
            <filter type="param_value" column="0" value="#" compare="startswith" keep="false"/>
            <filter type="param_value" ref="reference_genome.index" column="0"/>
          </option>
        </action>
      </when>
      <when value="history">
        <action type="metadata" name="dbkey">
          <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
        </action>
      </when>
    </conditional>
  </actions>
</data>

Format

The Bowtie 2 example also demonstrates conditionally setting an output format based on inputs, as shown below:

<data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
    <filter>(library['type'] == "paired" or library['type'] == "paired_collection") and library['unaligned_file'] is True</filter>
    <actions>
        <conditional name="library.type">
            <when value="paired">
                <action type="format">
                    <option type="from_param" name="library.input_2" param_attribute="ext" />
                </action>
            </when>
            <when value="paired_collection">
                <action type="format">
                    <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
                </action>
            </when>
        </conditional>
    </actions>
</data>

Unconditional Actions and Column Names

For a static file that contains a fixed number of columns, it is straight forward:

<outputs>
    <data format="tabular" name="table">
        <actions>
            <action name="column_names" type="metadata" default="Firstname,Lastname,Age" />
        </actions>
    </data>
</outputs>

It may also be necessary to use column names based on a variable from another input file. This is implemented in the htseq-count and featureCounts wrappers:

<inputs>
    <data name="input_file" type="data" multiple="false">
</inputs>
<outputs>
    <data format="tabular" name="output_short">
        <actions>
            <action name="column_names" type="metadata" default="Geneid,${input_file.name}" />
        </actions>
    </data>
</outputs>

Or in case of multiple files:

<inputs>
    <data name="input_files" type="data" multiple="true">
</inputs>
<outputs>
    <data format="tabular" name="output_short">
        <actions>
            <action name="column_names" type="metadata" default="Geneid,${','.join([a.name for a in $input_files])}" />
        </actions>
    </data>
</outputs>

Unconditional Actions - An Older Example

The first approach above to setting dbkey based on tool data tables is prefered, but an older example using so called “loc files” directly is found below.

In addition to demonstrating this lower-level direct access of .loc files, it demonstrates an unconditional action. The second block would not be needed for most cases - it was required in this tool to handle the specific case of a small reference file used for functional testing. It says that if the dbkey has been set to equCab2chrM (which is what the `<filter type="metadata_value"... column="1" /> tag does), then it should be changed to equCab2 (which is the <option type="from_param" ... column="0" ...> tag does).

<actions>
   <conditional name="refGenomeSource.genomeSource">
      <when value="indexed">
           <action type="metadata" name="dbkey">
            <option type="from_file" name="bowtie_indices.loc" column="0" offset="0">
               <filter type="param_value" column="0" value="#" compare="startswith" keep="false"/>
               <filter type="param_value" ref="refGenomeSource.index" column="1"/>
            </option>
         </action>
       </when>
    </conditional>
    <!-- Special casing equCab2chrM to equCab2 -->
    <action type="metadata" name="dbkey">
        <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
            <filter type="insert_column" column="0" value="equCab2chrM"/>
            <filter type="insert_column" column="0" value="equCab2"/>
            <filter type="metadata_value" ref="output" name="dbkey" column="1" />
        </option>
    </action>
</actions>

tool > outputs > data > actions > conditional

This directive is contained within an output data’s actions directive. This directive describes the state of the inputs required to apply an action (specified as children of the child when directives to this element) to an output.

See actions documentation for examples of this directive.

Attributes

Attribute	Details	Required
name	Name of the input parameter to base conditional logic on. The value of this parameter will be matched against nested when directives.	True

tool > outputs > data > actions > conditional > when

See actions documentation for examples of this directive.

Attributes

Attribute	Details	Required
value	Value to match conditional input value against.	False
``datatype_isinstance ``	Datatype to match against (if value is unspecified). This should be the short string describing the format (e.g. interval).	False

tool > outputs > data > actions > action

This directive is contained within an output data’s actions directive (either directly or beneath a parent conditional tag). This directive describes modifications to either the output’s format or metadata (based on whether type is format or metadata).

See actions documentation for examples of this directive.

Attributes

Attribute	Details	Required
type	Type of action (either format or metadata currently).	True
name	If type="metadata", the name of the metadata element.	False
default	If type="format", the default format if none of the nested options apply.	False

tool > outputs > data > discover_datasets

Describe datasets to dynamically collect after the job complete.

There are many simple tools with examples of this element distributed with Galaxy, including:

• https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output.xml
• https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_assign_primary.xml
• https://github.com/galaxyproject/galaxy/tree/master/test/functional/tools/multi_output_configured.xml

More information can be found on Planemo’s documentation for multiple output files.

Attributes

Attribute	Details	Required
from_provided_metad ata	Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort must not be set.	False
pattern	Regular expression used to find filenames and parse dynamic properties.	False
directory	Directory (relative to working directory) to search for files.	False
recurse	Indicates that the specified directory should be searched recursively for matching files.	False
format	Format (or datatype) of discovered datasets (an alias with ext).	False
ext	Format (or datatype) of discovered datasets (an alias with format).	False
visible	Indication if this dataset is visible in output history. This defaults to false, but probably shouldn’t - be sure to set to true if that is your intention.	False
assign_primary_outp ut	Replace the primary dataset described by the parameter data parameter with the first output discovered.	False

tool > outputs > collection

This tag set is contained within the <outputs> tag set, and it defines the output dataset collection description resulting from the tool’s execution. The value of the attribute label can be acquired from input parameters or metadata in the same way that the command line parameters are (discussed in the command directive).

Creating collections in tools is covered in-depth in planemo’s documentation.

Attributes

Attribute	Details	Required
name	Name for this output. This name is used as the Cheetah variable containing the Galaxy assigned output path in command and configfile elements. The name should not contain pipes or periods (e.g. .).	True
type	Collection type for output (e.g. paired, list, or list:list).	False
label	This will be the name of the history item for the output data set. The string can include structure like ${<some param name> .<some attribute>}, as discussed for command line parameters in the <command> tag set section above. The default label is ${tool.name} on ${o n_string}.	False
format_source	This is the name of input collection or dataset to derive output dataset collection’s element’s format/datatype from.	False
type_source	This is the name of input collection to derive collection’s type (e.g. collection_type) from.	False
structured_like	This is the name of input collection or dataset to derive “structure” of the output from (output element count and identifiers). For instance, if the referenced input has three ordered items with identifiers sample1, sample2, and sample3. If this references input elements in conditionals, this value should be qualified (e.g. cond|input instead of input if input is in a conditional with name="cond").	False
inherit_format	If structured_like is set, inherit format of outputs from format of corresponding input.	False

tool > outputs > collection > filter

The <data> tag can contain a <filter> tag which includes a Python code block to be executed to test whether to include this output in the outputs the tool ultimately creates. If the code, when executed, returns True, the output dataset is retained. In these code blocks the tool parameters appear as Python variables and are thus referred to without the $ used for the Cheetah template (used in the <command> tag). Variables that are part of conditionals are accessed using a hash named after the conditional.

Example

<inputs>
  <param type="data" format="fasta" name="reference_genome" label="Reference genome" />
  <param type="data" format="bam" name="input_bam" label="Aligned reads" />
  <conditional name="options">
    <param label="Use advanced options" name="selection_mode" type="select">
      <option selected="true" value="defaults">Use default options</option>
      <option value="advanced">Use advanced options</option>
    </param>
    <when value="defaults"> </when>
    <when value="advanced">
      <param name="vcf_output" type="boolean" checked="false" label="VCF output"
        truevalue="--vcf" falsevalue="" />
    </when>
  <conditional>
</inputs>
<outputs>
  <data format="txt" label="Alignment report on ${on_string}" name="output_txt" />
  <data format="vcf" label="Variant summary on ${on_string}" name="output_vcf">
      <filter>options['selection_mode'] == 'advanced' and options['vcf_output']</filter>
  </data>
</outputs>

tool > outputs > collection > discover_datasets

This tag allows one to describe the datasets contained within an output collection dynamically, such that the outputs are “discovered” based on regular expressions after the job is complete.

There are many simple tools with examples of this element distributed with Galaxy, including:

• https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_split_on_column.xml
• https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
• https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/collection_creates_dynamic_nested.xml

Attributes

Attribute	Details	Required
from_provided_metad ata	Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort must not be set.	False
pattern	Regular expression used to find filenames and parse dynamic properties.	False
directory	Directory (relative to working directory) to search for files.	False
format	Format (or datatype) of discovered datasets (an alias with ext).	False
ext	Format (or datatype) of discovered datasets (an alias with format).	False
visible	Indication if this dataset is visible in output history. This defaults to false, but probably shouldn’t - be sure to set to true if that is your intention.	False

tool > tests

Container tag set to specify tests via the tag sets. Any number of tests can be included, and each test is wrapped within separate tag sets. Functional tests are executed via Planemo or the run_tests.sh shell script distributed with Galaxy.

The documentation contained here is mostly reference documentation, for tutorials on writing tool tests please check out Planemo’s Test-Driven Development documentation or the much older wiki content for WritingTests.

Best Practices

Find the Intergalactic Utilities Commision suggested best practices for this element here.

tool > tests > test

This tag set contains the necessary parameter values for executing the tool via the functional test framework.

Example

The following two tests will execute the /tools/filters/sorter.xml tool. Notice the way that the tool’s inputs and outputs are defined.

<tests>
  <test>
    <param name="input" value="1.bed" ftype="bed" />
    <param name="column" value="1"/>
    <param name="order" value="ASC"/>
    <param name="style" value="num"/>
    <output name="out_file1" file="sort1_num.bed" ftype="bed" />
  </test>
  <test>
    <param name="input" value="7.bed" ftype="bed" />
    <param name="column" value="1"/>
    <param name="order" value="ASC"/>
    <param name="style" value="alpha"/>
    <output name="out_file1" file="sort1_alpha.bed" ftype="bed" />
  </test>
</tests>

The following example, tests the execution of the MAF-to-FASTA converter (/tools/maf/maf_to_fasta.xml).

<tests>
    <test>
        <param name="input1" value="3.maf" ftype="maf"/>
        <param name="species" value="canFam1"/>
        <param name="fasta_type" value="concatenated"/>
        <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>
    </test>
</tests>

This test demonstrates verifying specific properties about a test output instead of directly comparing it to another file. Here the file attribute is not specified and instead a series of assertions is made about the output.

<test>
    <param name="input" value="maf_stats_interval_in.dat" />
    <param name="lineNum" value="99999"/>
    <output name="out_file1">
        <assert_contents>
            <has_text text="chr7" />
            <not_has_text text="chr8" />
            <has_text_matching expression="1274\d+53" />
            <has_line_matching expression=".*\s+127489808\s+127494553" />
            <!-- &#009; is XML escape code for tab -->
            <has_line line="chr7&#009;127471195&#009;127489808" />
            <has_n_columns n="3" />
        </assert_contents>
    </output>
</test>

Attributes

Attribute	Details	Required
expect_exit_code	Describe the job’s expected exit code.	False
``expect_num_outputs` `	Assert the number of outputs this test should produce, this is useful to ensure filter directives are implemented correctly.	False
expect_failure	Setting this to true indicates the expectation is for the job fail. If set to true no job output checks may be present in test definition.	False
maxseconds	Maximum amount of time to let test run.	False

tool > tests > test > param

This tag set defines the tool’s input parameters for executing the tool via the functional test framework. See test documentation for some simple examples of parameters.

Attributes

Attribute	Details	Required
name	This value must match the name of the associated input parameter (param).	True
value	This value must be one of the legal values that can be assigned to an input parameter.	False
ftype	This attribute name should be included only with parameters of type data for the tool. If this attribute name is not included, the functional test framework will attempt to determine the data type for the input dataset using the data type sniffers.	False
dbkey	Specifies a dbkey value for the referenced input dataset. This is only valid if the corresponding parameter is of type data.	False

tool > tests > test > repeat

Specify test parameters below an iteration of a repeat block with this element.

param elements in a test block can be arranged into nested repeat, conditional, and select structures to match the inputs. While this might be overkill for simple tests, it helps prevent ambiguous definitions and keeps things organized in large test cases. A future profile version of Galaxy tools may require repeat blocks be explicitly defined with this directive.

Examples

The test tool disambiguate_repeats.xml demonstrates the use of this directive.

This first test case demonstrates that this block allows different values for the param named input to be tested even though this parameter name appears in two different <repeat> elements in the <inputs> definition.

<!-- Can disambiguate repeats and specify multiple blocks using,
     nested structure. -->
<test>
    <repeat name="queries">
        <param name="input" value="simple_line.txt"/>
    </repeat>
    <repeat name="more_queries">
        <param name="input" value="simple_line_alternative.txt"/>
    </repeat>
    <output name="out_file1">
        <assert_contents>
            <has_line line="This is a line of text." />
            <has_line line="This is a different line of text." />
        </assert_contents>
    </output>
</test>

The second definition in that file demonstrates repeated <repeat> blocks allowing multiple instances of a single repeat to be specified.

<!-- Multiple such blocks can be specified but only with newer API
     driven tests. -->
<test>
    <repeat name="queries">
        <param name="input" value="simple_line.txt"/>
    </repeat>
    <repeat name="queries">
        <param name="input" value="simple_line_alternative.txt"/>
    </repeat>
    <repeat name="more_queries">
        <param name="input" value="simple_line.txt"/>
    </repeat>
    <repeat name="more_queries">
        <param name="input" value="simple_line_alternative.txt"/>
    </repeat>
    <output name="out_file1" file="simple_lines_interleaved.txt"/>
</test>

Attributes

Attribute	Details	Required
name	This value must match the name of the associated input repeat.	True

tool > tests > test > section

Specify test parameters below a named of a section block matching one in inputs with this element.

param elements in a test block can be arranged into nested repeat, conditional, and select structures to match the inputs. While this might be overkill for simple tests, it helps prevent ambiguous definitions and keeps things organized in large test cases. A future profile version of Galaxy tools may require section blocks be explicitly defined with this directive.

Examples

The test tool demonstrating sections (section.xml) contains a test case demonstrating this block. This test case appears below:

<test>
    <section name="int">
        <param name="inttest" value="12456" />
    </section>
    <section name="float">
        <param name="floattest" value="6.789" />
    </section>
    <output name="out_file1">
        <assert_contents>
            <has_line line="12456" />
            <has_line line="6.789" />
        </assert_contents>
    </output>
</test>

Attributes

Attribute	Details	Required
name	This value must match the name of the associated input section.	True

tool > tests > test > conditional

Specify test parameters below a named of a conditional block matching one in inputs with this element.

param elements in a test block can be arranged into nested repeat, conditional, and select structures to match the inputs. While this might be overkill for simple tests, it helps prevent ambiguous definitions and keeps things organized in large test cases. A future profile version of Galaxy tools may require conditional blocks be explicitly defined with this directive.

Examples

The following example demonstrates disambiguation of a parameter (named use) which appears in multiple param names in conditionals in the inputs definition of the disambiguate_cond.xml tool.

<!-- Can use nested conditional blocks as shown below to disambiguate
     various nested parameters. -->
<test>
    <conditional name="p1">
        <param name="use" value="False"/>
    </conditional>
    <conditional name="p2">
        <param name="use" value="True"/>
    </conditional>
    <conditional name="p3">
        <param name="use" value="False"/>
    </conditional>
    <conditional name="files">
        <param name="attach_files" value="True" />
        <conditional name="p4">
            <param name="use" value="True"/>
            <param name="file" value="simple_line_alternative.txt" />
        </conditional>
    </conditional>
    <output name="out_file1">
        <assert_contents>
            <has_line line="7 4 7" />
            <has_line line="This is a different line of text." />
        </assert_contents>
    </output>
</test>

The tophat2 tool demonstrates a real tool that benefits from more structured test cases using the conditional test directive. One such test case from that tool is shown below.

<!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
<test>
    <!-- TopHat commands:
    tophat2 -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search +report_discordant_pairs tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
    Replace the + with double-dash
    Rename the files in tmp_dir appropriately
    -->
    <conditional name="singlePaired">
      <param name="sPaired" value="paired"/>
      <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
      <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
      <param name="mate_inner_distance" value="20"/>
      <param name="report_discordant_pairs" value="Yes" />
    </conditional>
    <param name="genomeSource" value="indexed"/>
    <param name="index" value="tophat_test"/>
    <conditional name="params">
      <param name="settingsType" value="full"/>
      <param name="library_type" value="FR Unstranded"/>
      <param name="read_mismatches" value="5"/>
      <!-- Error: the read mismatches (5) and the read gap length (2) should be less than or equal to the read edit dist (2) -->
      <param name="read_edit_dist" value="5" />
      <param name="bowtie_n" value="Yes"/>
      <param name="mate_std_dev" value="20"/>
      <param name="anchor_length" value="8"/>
      <param name="splice_mismatches" value="0"/>
      <param name="min_intron_length" value="70"/>
      <param name="max_intron_length" value="500000"/>
      <param name="max_multihits" value="40"/>
      <param name="min_segment_intron" value="50" />
      <param name="max_segment_intron" value="500000" />
      <param name="seg_mismatches" value="2"/>
      <param name="seg_length" value="25"/>
      <conditional name="indel_search">
        <param name="allow_indel_search" value="No"/>
      </conditional>
      <conditional name="own_junctions">
        <param name="use_junctions" value="Yes" />
        <conditional name="gene_model_ann">
          <param name="use_annotations" value="No" />
        </conditional>
        <conditional name="raw_juncs">
          <param name="use_juncs" value="No" />
        </conditional>
        <conditional name="no_novel_juncs">
          <param name="no_novel_juncs" value="No" />
        </conditional>
      </conditional>
      <conditional name="coverage_search">
        <param name="use_search" value="No" />
      </conditional>
      <param name="microexon_search" value="Yes" />
      <conditional name="bowtie2_settings">
        <param name="b2_settings" value="No" />
      </conditional>
      <!-- Fusion search params -->
      <conditional name="fusion_search">
        <param name="do_search" value="Yes" />
        <param name="anchor_len" value="21" />
        <param name="min_dist" value="10000021" />
        <param name="read_mismatches" value="3" />
        <param name="multireads" value="4" />
        <param name="multipairs" value="5" />
        <param name="ignore_chromosomes" value="chrM"/>
      </conditional>
    </conditional>
    <conditional name="readGroup">
      <param name="specReadGroup" value="no" />
    </conditional>
    <output name="junctions" file="tophat2_out4j.bed" />
    <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
</test>

Attributes

Attribute	Details	Required
name	This value must match the name of the associated input conditional.	True

tool > tests > test > output

This tag set defines the variable that names the output dataset for the functional test framework. The functional test framework will execute the tool using the parameters defined in the <param> tag sets and generate a temporary file, which will either be compared with the file named in the file attribute value or checked against assertions made by a child assert_contents tag to verify that the tool is functionally correct.

Attributes

Attribute	Details	Required
name	This value is the same as the value of the name attribute of the <data> tag set contained within the tool’s <outputs> tag set.	False
file	If specified, this value is the name of the output file stored in the target test-data directory which will be used to compare the results of executing the tool via the functional test framework.	False
ftype	If specified, this value will be checked against the corresponding output’s data type. If these do not match, the test will fail.	False
sort	This flag causes the lines of the output to be sorted before they are compared to the expected output. This could be useful for non-deterministic output.	False
value	An alias for file.	False
md5	If specified, the target output’s MD5 hash should match the value specified here. For large static files it may be inconvenient to upload the entiry file and this can be used instead.	False
checksum	If specified, the target output’s checksum should match the value specified here. This value should have the form hash_type:hash_valu e (e.g. sha1:8156d7ca0f46ed 7abac98f82e36cfaddb2a ca041). For large static files it may be inconvenient to upload the entiry file and this can be used instead.	False
compare	Type of comparison to use when comparing test generated output files to expected output files. Currently valid value are diff (the default), re_match, sim_size, re_match_multiline` `, and ``contains.	False
lines_diff	If compare is set to diff, the number of lines of difference to allow (each line with a modification is a line added and a line removed so this counts as two lines).	False
decompress	If compare is set to diff, attempt to decompress both produced output and expected output files if needed before performing the diff. This flag is useful for testing gzipped outputs that are non-deterministic despite having deterministic decompressed contents. This is available in Galaxy 17.05+ and was introduced in pull request #3550.	False
delta	If compare is set to sim_size, this is the number of bytes different allowed.	False

tool > tests > test > output > discover_dataset

This directive specifies a test for an output’s discovered dataset. It acts as an output test tag in many ways and can define any tests of that tag (e.g. assert_contents, value, compare, md5, checksum, metadata, etc…).

Example

The functional test tool multi_output_assign_primary.xml provides a demonstration of using this tag.

<test>
  <param name="num_param" value="7" />
  <param name="input" ftype="txt" value="simple_line.txt"/>
  <output name="sample">
    <assert_contents>
      <has_line line="1" />
    </assert_contents>
    <!-- no sample1 it was consumed by named output "sample" -->
    <discovered_dataset designation="sample2" ftype="tabular">
      <assert_contents><has_line line="2" /></assert_contents>
    </discovered_dataset>
    <discovered_dataset designation="sample3" ftype="tabular">
      <assert_contents><has_line line="3" /></assert_contents>
    </discovered_dataset>
  </output>
</test>

Attributes

Attribute	Details	Required
designation	The designation of the discovered dataset.	False

tool > tests > test > output > metadata

This directive specifies a test for an output’s metadata as an expected key-value pair.

Example

The functional test tool tool_provided_metadata_1.xml provides a demonstration of using this tag.

<test>
  <param name="input1" value="simple_line.txt" />
  <output name="out1" file="simple_line.txt" ftype="txt">
    <metadata name="name" value="my dynamic name" />
    <metadata name="info" value="my dynamic info" />
    <metadata name="dbkey" value="cust1" />
  </output>
</test>

Attributes

Attribute	Details	Required
name	Name of the metadata element to check.	True
value	Expected value (as a string) of metadata value.	True

tool > tests > test > output > assert_contents

This tag set defines a sequence of checks or assertions to run against the target output. This tag requires no attributes, but child tags should be used to define the assertions to make about the output. The functional test framework makes it easy to extend Galaxy with such tags, the following table summarizes many of the default assertion tags that come with Galaxy and examples of each can be found below.

The implementation of these tags are simply Python functions defined in the /lib/galaxy/tools/verify/asserts module.

Child Element/Assertion	Details
has_text	Asserts the specified text appears in the output (e.g. <has_text text="chr7">).
not_has_text	Asserts the specified text does not appear in the output (e.g. <not_has_text text="chr8" />) .
has_text_matching	Asserts text matching the specified regular expression (expression) appears in the output (e.g. <has_text_matching expression=" 1274\d+53" /> ).
has_line	Asserts a line matching the specified string (line) appears in the output (e.g. <has_line line="A full example line." />).
has_line_matching	Asserts a line matching the specified regular expression (expression) appears in the output (e.g. <has_line_matching expression=" .*\s+127489808\s+127494553" />) .
has_n_columns	Asserts tabular output contains the specified number (n) of columns (e.g. <has_n_columns n="3" />).
is_valid_xml	Asserts the output is a valid XML file (e.g. <is_valid_xml />).
has_element_with_path	Asserts the XML output contains at least one element (or tag) with the specified XPath-like path (e.g. <has_element_with_path path="Bl astOutput_param/Parameters/Parame ters_matrix" />).
has_n_elements_with_path	Asserts the XML output contains the specified number (n) of elements (or tags) with the specified XPath-like path (e.g. ``<has_n_elements_with_path n=”9” path=”BlastOutput_iterations/Ite ration/Iteration_hits/Hit/Hit_num ” />``).
element_text_is	Asserts the text of the XML element with the specified XPath-like path is the specified text (e.g. <element_text_is path="BlastOut put_program" text="blastp" />).
element_text_matches	Asserts the text of the XML element with the specified XPath-like path matches the regular expression defined by expression (e.g. <element_text_matches path="Bla stOutput_version" expression="BLA STP\s+2\.2.*" />).
attribute_is	Asserts the XML attribute for the element (or tag) with the specified XPath-like path is the specified text (e.g. <attribute_is path="outerElemen t/innerElement1" attribute="foo" text="bar" /> ).
attribute_matches	Asserts the XML attribute for the element (or tag) with the specified XPath-like path matches the regular expression specified by expression (e.g. <attribute_matches path="outerE lement/innerElement2" attribute=" foo2" expression="bar\d+" />).
element_text	This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like path (e.g. ``<element_text path=”BlastOutput _iterations/Iteration/Iteration_h its/Hit/Hit_def”><not_has_text te xt=”EDK72998.1” /></element_text> ``).

Examples

The following demonstrtes a wide variety of text-based and tabular assertion statements.

<output name="out_file1">
    <assert_contents>
        <has_text text="chr7" />
        <not_has_text text="chr8" />
        <has_text_matching expression="1274\d+53" />
        <has_line_matching expression=".*\s+127489808\s+127494553" />
        <!-- &#009; is XML escape code for tab -->
        <has_line line="chr7&#009;127471195&#009;127489808" />
        <has_n_columns n="3" />
    </assert_contents>
</output>

The following demonstrtes a wide variety of XML assertion statements.

<output name="out_file1">
    <assert_contents>
        <is_valid_xml />
        <has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
        <has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
        <element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*" />
        <element_text_is path="BlastOutput_program" text="blastp" />
        <element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
            <not_has_text text="EDK72998.1" />
            <has_text_matching expression="ABK[\d\.]+" />
        </element_text>
    </assert_contents>
</output>

The following demonstrtes verifying XML content with XPath-like expressions.

<output name="out_file1">
    <assert_contents>
        <attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
        <attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />
    </assert_contents>
</output>

tool > tests > test > output_collection

Define tests for extra files corresponding to an output collection.

output_collection directives should specify a name and type attribute to describe the expected output collection as a whole.

Expectations about collection contents are described using child element directives. For nested collections, these child element directives may themselves contain children.

Examples

The genetrack tool demonstrates basic usage of an output_collection test expectation.

<test>
    <param name="input" value="genetrack_input2.gff" ftype="gff" />
    <param name="input_format" value="gff" />
    <param name="sigma" value="5" />
    <param name="exclusion" value="20" />
    <param name="up_width" value="10" />
    <param name="down_width" value="10" />
    <param name="filter" value="3" />
    <output_collection name="genetrack_output" type="list">
        <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
    </output_collection>
</test>

The CWPair2 tool demonstrates that elements can specify a compare attribute just like output.

<test>
    <param name="input" value="cwpair2_input1.gff" />
    <param name="up_distance" value="25" />
    <param name="down_distance" value="100" />
    <param name="method" value="all" />
    <param name="binsize" value="1" />
    <param name="threshold_format" value="relative_threshold" />
    <param name="relative_threshold" value="0.0" />
    <param name="output_files" value="matched_pair" />
    <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
    <output_collection name="MP" type="list">
        <element name="data_MP_closest_f0u25d100_on_data_1.gff" file="closest_mp_output1.gff" ftype="gff" compare="contains"/>
        <element name="data_MP_largest_f0u25d100_on_data_1.gff" file="largest_mp_output1.gff" ftype="gff" compare="contains"/>
        <element name="data_MP_mode_f0u25d100_on_data_1.gff" file="mode_mp_output1.gff" ftype="gff" compare="contains"/>
    </output_collection>
</test>

The collection_creates_dynamic_nested test tool demonstrates the use of nested element directives as described above. Notice also that it tests the output with assert_contents instead of supplying a file attribute. Like hinted at with with compare attribute above, the element tag can specify any of the test attributes that apply to the output (e.g. md5, compare, diff, etc…).

<test>
  <param name="foo" value="bar" />
  <output_collection name="list_output" type="list:list">
    <element name="oe1">
      <element name="ie1">
        <assert_contents>
          <has_text_matching expression="^A\n$" />
        </assert_contents>
      </element>
      <element name="ie2">
        <assert_contents>
          <has_text_matching expression="^B\n$" />
        </assert_contents>
      </element>
    </element>
    <element name="oe2">
      <element name="ie1">
        <assert_contents>
          <has_text_matching expression="^C\n$" />
        </assert_contents>
      </element>
      <element name="ie2">
        <assert_contents>
          <has_text_matching expression="^D\n$" />
        </assert_contents>
      </element>
    </element>
    <element name="oe3">
      <element name="ie1">
        <assert_contents>
          <has_text_matching expression="^E\n$" />
        </assert_contents>
      </element>
      <element name="ie2">
        <assert_contents>
          <has_text_matching expression="^F\n$" />
        </assert_contents>
      </element>
    </element>
  </output_collection>
</test>

Attributes

Attribute	Details	Required
name	This value is the same as the value of the name attribute of the <collection> tag set contained within the tool’s <outputs> tag set.	True
type	Expected collection type (e.g. list, paired, or list:paired).	False
count	Number of elements in output collection.	False

tool > tests > test > assert_command

Describe assertions about the job’s generated command-line.

This tag set defines a sequence of checks or assertions to run against the target output. This tag requires no attributes, but child tags should be used to define the assertions to make about the output. The functional test framework makes it easy to extend Galaxy with such tags, the following table summarizes many of the default assertion tags that come with Galaxy and examples of each can be found below.

The implementation of these tags are simply Python functions defined in the /lib/galaxy/tools/verify/asserts module.

Child Element/Assertion	Details
has_text	Asserts the specified text appears in the output (e.g. <has_text text="chr7">).
not_has_text	Asserts the specified text does not appear in the output (e.g. <not_has_text text="chr8" />) .
has_text_matching	Asserts text matching the specified regular expression (expression) appears in the output (e.g. <has_text_matching expression=" 1274\d+53" /> ).
has_line	Asserts a line matching the specified string (line) appears in the output (e.g. <has_line line="A full example line." />).
has_line_matching	Asserts a line matching the specified regular expression (expression) appears in the output (e.g. <has_line_matching expression=" .*\s+127489808\s+127494553" />) .
has_n_columns	Asserts tabular output contains the specified number (n) of columns (e.g. <has_n_columns n="3" />).
is_valid_xml	Asserts the output is a valid XML file (e.g. <is_valid_xml />).
has_element_with_path	Asserts the XML output contains at least one element (or tag) with the specified XPath-like path (e.g. <has_element_with_path path="Bl astOutput_param/Parameters/Parame ters_matrix" />).
has_n_elements_with_path	Asserts the XML output contains the specified number (n) of elements (or tags) with the specified XPath-like path (e.g. ``<has_n_elements_with_path n=”9” path=”BlastOutput_iterations/Ite ration/Iteration_hits/Hit/Hit_num ” />``).
element_text_is	Asserts the text of the XML element with the specified XPath-like path is the specified text (e.g. <element_text_is path="BlastOut put_program" text="blastp" />).
element_text_matches	Asserts the text of the XML element with the specified XPath-like path matches the regular expression defined by expression (e.g. <element_text_matches path="Bla stOutput_version" expression="BLA STP\s+2\.2.*" />).
attribute_is	Asserts the XML attribute for the element (or tag) with the specified XPath-like path is the specified text (e.g. <attribute_is path="outerElemen t/innerElement1" attribute="foo" text="bar" /> ).
attribute_matches	Asserts the XML attribute for the element (or tag) with the specified XPath-like path matches the regular expression specified by expression (e.g. <attribute_matches path="outerE lement/innerElement2" attribute=" foo2" expression="bar\d+" />).
element_text	This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like path (e.g. ``<element_text path=”BlastOutput _iterations/Iteration/Iteration_h its/Hit/Hit_def”><not_has_text te xt=”EDK72998.1” /></element_text> ``).

tool > tests > test > assert_stdout

Describe assertions about the job’s standard output.

This tag set defines a sequence of checks or assertions to run against the target output. This tag requires no attributes, but child tags should be used to define the assertions to make about the output. The functional test framework makes it easy to extend Galaxy with such tags, the following table summarizes many of the default assertion tags that come with Galaxy and examples of each can be found below.

The implementation of these tags are simply Python functions defined in the /lib/galaxy/tools/verify/asserts module.

Child Element/Assertion	Details
has_text	Asserts the specified text appears in the output (e.g. <has_text text="chr7">).
not_has_text	Asserts the specified text does not appear in the output (e.g. <not_has_text text="chr8" />) .
has_text_matching	Asserts text matching the specified regular expression (expression) appears in the output (e.g. <has_text_matching expression=" 1274\d+53" /> ).
has_line	Asserts a line matching the specified string (line) appears in the output (e.g. <has_line line="A full example line." />).
has_line_matching	Asserts a line matching the specified regular expression (expression) appears in the output (e.g. <has_line_matching expression=" .*\s+127489808\s+127494553" />) .
has_n_columns	Asserts tabular output contains the specified number (n) of columns (e.g. <has_n_columns n="3" />).
is_valid_xml	Asserts the output is a valid XML file (e.g. <is_valid_xml />).
has_element_with_path	Asserts the XML output contains at least one element (or tag) with the specified XPath-like path (e.g. <has_element_with_path path="Bl astOutput_param/Parameters/Parame ters_matrix" />).
has_n_elements_with_path	Asserts the XML output contains the specified number (n) of elements (or tags) with the specified XPath-like path (e.g. ``<has_n_elements_with_path n=”9” path=”BlastOutput_iterations/Ite ration/Iteration_hits/Hit/Hit_num ” />``).
element_text_is	Asserts the text of the XML element with the specified XPath-like path is the specified text (e.g. <element_text_is path="BlastOut put_program" text="blastp" />).
element_text_matches	Asserts the text of the XML element with the specified XPath-like path matches the regular expression defined by expression (e.g. <element_text_matches path="Bla stOutput_version" expression="BLA STP\s+2\.2.*" />).
attribute_is	Asserts the XML attribute for the element (or tag) with the specified XPath-like path is the specified text (e.g. <attribute_is path="outerElemen t/innerElement1" attribute="foo" text="bar" /> ).
attribute_matches	Asserts the XML attribute for the element (or tag) with the specified XPath-like path matches the regular expression specified by expression (e.g. <attribute_matches path="outerE lement/innerElement2" attribute=" foo2" expression="bar\d+" />).
element_text	This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like path (e.g. ``<element_text path=”BlastOutput _iterations/Iteration/Iteration_h its/Hit/Hit_def”><not_has_text te xt=”EDK72998.1” /></element_text> ``).

tool > tests > test > assert_stderr

Describe assertions about the job’s standard error.

This tag set defines a sequence of checks or assertions to run against the target output. This tag requires no attributes, but child tags should be used to define the assertions to make about the output. The functional test framework makes it easy to extend Galaxy with such tags, the following table summarizes many of the default assertion tags that come with Galaxy and examples of each can be found below.

The implementation of these tags are simply Python functions defined in the /lib/galaxy/tools/verify/asserts module.

Child Element/Assertion	Details
has_text	Asserts the specified text appears in the output (e.g. <has_text text="chr7">).
not_has_text	Asserts the specified text does not appear in the output (e.g. <not_has_text text="chr8" />) .
has_text_matching	Asserts text matching the specified regular expression (expression) appears in the output (e.g. <has_text_matching expression=" 1274\d+53" /> ).
has_line	Asserts a line matching the specified string (line) appears in the output (e.g. <has_line line="A full example line." />).
has_line_matching	Asserts a line matching the specified regular expression (expression) appears in the output (e.g. <has_line_matching expression=" .*\s+127489808\s+127494553" />) .
has_n_columns	Asserts tabular output contains the specified number (n) of columns (e.g. <has_n_columns n="3" />).
is_valid_xml	Asserts the output is a valid XML file (e.g. <is_valid_xml />).
has_element_with_path	Asserts the XML output contains at least one element (or tag) with the specified XPath-like path (e.g. <has_element_with_path path="Bl astOutput_param/Parameters/Parame ters_matrix" />).
has_n_elements_with_path	Asserts the XML output contains the specified number (n) of elements (or tags) with the specified XPath-like path (e.g. ``<has_n_elements_with_path n=”9” path=”BlastOutput_iterations/Ite ration/Iteration_hits/Hit/Hit_num ” />``).
element_text_is	Asserts the text of the XML element with the specified XPath-like path is the specified text (e.g. <element_text_is path="BlastOut put_program" text="blastp" />).
element_text_matches	Asserts the text of the XML element with the specified XPath-like path matches the regular expression defined by expression (e.g. <element_text_matches path="Bla stOutput_version" expression="BLA STP\s+2\.2.*" />).
attribute_is	Asserts the XML attribute for the element (or tag) with the specified XPath-like path is the specified text (e.g. <attribute_is path="outerElemen t/innerElement1" attribute="foo" text="bar" /> ).
attribute_matches	Asserts the XML attribute for the element (or tag) with the specified XPath-like path matches the regular expression specified by expression (e.g. <attribute_matches path="outerE lement/innerElement2" attribute=" foo2" expression="bar\d+" />).
element_text	This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like path (e.g. ``<element_text path=”BlastOutput _iterations/Iteration/Iteration_h its/Hit/Hit_def”><not_has_text te xt=”EDK72998.1” /></element_text> ``).

tool > help

This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html .

tag	details
.. class:: warni ngmark	a yellow warning symbol
.. class:: infom ark	a blue information symbol
``.. image:: path- of-the-file.png :h eight: 500 :width: 600``	insert a png file of height 500 and width 600 at this position
**bold**	bold
*italic*	italic
*	list
-	list
::	paragraph
-----	a horizontal line

Examples

Show a warning sign to remind users that this tool accept fasta format files only, followed by an example of the query sequence and a figure.

<help>

.. class:: warningmark

'''TIP''' This tool requires *fasta* format.

----

'''Example'''

Query sequence::
    >seq1
    ATCG...

.. image:: my_figure.png
    :height: 500
    :width: 600

</help>

Best Practices

Find the Intergalactic Utilities Commision suggested best practices for this element here.

tool > citations

Tool files may declare one citations element. Each citations element can contain one or more citation tag elements - each of which specifies tool citation information using either a DOI or a BibTeX entry.

These citations will appear at the bottom of the tool form in a formatted way but the user will have to option to select RAW BibTeX for copying and pasting as well. Likewise, the history menu includes an option allowing users to aggregate all such citations across an analysis in a list of citations.

BibTeX entries for citations annotated with DOIs will be fetched by Galaxy from https://dx.doi.org/ and cached.

<citations>
   <!-- Example of annotating a citation using a DOI. -->
   <citation type="doi">10.1093/bioinformatics/btq281</citation>

   <!-- Example of annotating a citation using a BibTex entry. -->
   <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
   author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
   title = {An interior-point method for large-scale l1-regularized logistic regression},
   journal = {Journal of Machine Learning Research},
   year = {2007},
   volume = {8},
   pages = {1519-1555}
   }</citation>
 </citations>

For more implementation information see the pull request adding this feature. For more examples of how to add this to tools checkout the following commits adding this to the NCBI BLAST+ suite, phenotype association tools, MAF suite, and MACS2 suite.

This feature was added to the August 2014 release of Galaxy, tools annotated with citations will work in older releases of Galaxy but no citation information will be available to the end user.

tool > citations > citation

Each citations element can contain one or more citation tag elements - each of which specifies tool citation information using either a DOI or a BibTeX entry.

Attributes

Attribute	Details	Required
type	Type of citation - currently doi and bibtex are the only supported options.	True