Tool Panel Administration

The Galaxy tool panel is located on the left of the ‘Analysis page’ and offers the following ways of modification.

Configuration

The contents of the tool panel are defined by the following configuration files.

Three configuration options define the content of the toolbox:

  • tool_config_file (default: tool_conf.xml)

  • shed_tool_config_file (default: shed_tool_conf.xml)

  • migrated_tools_config (default migrated_tools_conf.xml)

Built-in and custom tools

Built-in tools are defined in the file tool_conf.xml.sample which is loaded by default. This is because of the default value of the tool_config_file configuration setting in the galaxy.yml file which is tool_conf.xml (Galaxy loads the sample file automatically when tool_conf.xml is absent).

Further custom tool config files can be listed in tool_config_file. These files could for instance contain custom local tools that are not installed from the ToolShed. Note that, if custom tool config files are listed, then this list also should contain a tool configuration file containing the built-in tools. It’s favorable to just use tool_conf.xml.sample to obtain automatic updates for built-in tools.

It’s important to note that the tool configuration files, i.e. the sections, labels, and tools included in them, are added in the order in which they are specified. Therefore, to setup the order of the sections and labels a custom tool conf file (e.g. tool_conf_labels.xml) which contains only the sections and labels appearing in any other tool config file can be used.

Since tools and sections are added in the order of installation and modifying large XML files is tedious, the following setup should cover most instances:

tool_config_file: tool_conf_labels.xml,tool_conf.xml.sample

A section containing built-in converters can be added to the tool panel by enabling the display_builtin_converters setting.

Tool Shed tools

Tools that are installed from a Tool Shed, are added to the file named by the shed_tool_config_file configuration setting.

Migrated tools

The migrated_tools_conf.xml(.sample) can typically be ignored, it’s used for local tool repositories that have been moved to the ToolShed. The configuration file migrated_tools_conf.xml.sample is in the Galaxy configuration directory. If you start your Galaxy server using sh run.sh or something similar, this sample file will automatically be copied to a file named migrated_tools_conf.xml in the same directory. You’ll be required to manually copy this file if you start your Galaxy server differently. The migrated_tools_conf.xml file is reserved to contain the XML tag sets for repositories that contain tools that were once included in the Galaxy distribution but have been moved to the Tool Shed. Similar to the approach used with the other shed-related tool panel configuration files described above, this file’s contents will be changed automatically for certain tools contained in repositories that are installed into your local Galaxy instance.

Layout

The various tool configuration files described in the previous section are all used to load tool panel items (tools, sections, labels, and workflows). A file named integrated_tool_panel.xml defines the arrangement for displaying these loaded items in your Galaxy tool panel. If this file does not exist in your Galaxy installation directory, it will be automatically created and populated when you start your Galaxy server. It is initially populated based on the order in which the tool panel items are loaded. The items are loaded as each tool panel configuration file is parsed and its items are loaded. The order in which these configuration files are parsed is the order of the comma-separated list of files defined in your tool_config_file setting in your config/galaxy.yml configuration file. The migrated_tools_conf.xml file is always parsed and loaded last.

If you uninstall a repository that contains tools, entries for those tools will automatically be removed from the shed-related tool panel config file and the integrated_tool_panel.xml file.

The best approach for managing the integrated_tool_panel.xml file is to allow Galaxy to add or remove entries as manually adding or removing them will likely result in undesired behavior. The order of sections and labels can be changed using a tool_conf_labels.xml file as described above.

Tool conf XML syntax

A tool configuration file is an XML file containing mainly four elements:

  1. toolbox is the root tag. It has two optional attributes:

  • tool_path is used to set the path (relative to Galaxy’s root dir) containing the tools.

  • monitor is a boolean that indicates if Galaxy should monitor changes to the file.

  1. section defines a section in the tool panel. It needs to have an id attribute which should have no spaces, and has an optional name attribute which defines the text shown to the user (otherwise id is used.)

  2. label adds a header line to the tool panel. It needs to have an id attribute and optionally define a text attribute which gives the text shown to the user.

  3. tool defines a tool.

  • The file attribute gives the path to the tool XML file (relative to the tool_path of the toolbox).

  • An optional labels render a label next to the tool in the tool panel, e.g. labels="updated".

  • An additional guid attribute is set by Galaxy for tools installed from a ToolShed.

Typically section and label tags are used as child of toolbox, and tools are used as child of section. In the following two examples are shown.

<toolbox monitor="true">
  <label id="general_text_label" text="General Text Tools" />
  <section id="getext" name="Get Data">
    <tool file="data_source/upload.xml" />
  </section>
</toolbox>

<toolbox tool_path="shed_tools">
    <section id="metagenomics" name="Metagenomics" version="">
        <tool file="toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/2d4c0825cfe6/picrust_predict_metagenomes/predict_metagenomes.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.0.1.0">
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>picrust_predict_metagenomes</repository_name>
            <repository_owner>iuc</repository_owner>
            <installed_changeset_revision>2d4c0825cfe6</installed_changeset_revision>
            <id>toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.0.1.0</id>
            <version>1.0.1.0</version>
        </tool>
    </section>
</toolbox>

Tool panel views

For large Galaxy instances the tool panel typically grows to hundreds of tools, which makes it inconvenient to use. Also, the structure of the tool panel is difficult to change using the XML files.

Tool panel views allow admins to define custom static tool panels, i.e. subsets of the tools in a custom easy-to-define structure. In addition, some automatically structured tool panel views are generated by Galaxy itself. At the moment these are the tool panel views defined by the EDAM ontology (see configuration edam_panel_views).

The static admin-defined tool panel views are defined by YAML files contained in the directory specified by panel_views_dir. A default tool panel views can be defined by default_tool_panel.

The following example defines a tool panel view rna_analysis that will be shown to the user as "RNA Analysis". The tool panel view just uses existing sections as they are.

name: RNA Analysis
id: rna_analysis
type: activity
items:
- label: General Tools
- sections: [text_manipulation, get_data,collection_operations,convert_formats,expression_tools]
- label: NGS Tools
- sections: [deeptools,bed,sam_bam,fasta_fastq,mapping]
- label: RNA Analysis
- section: rna_seq
- section: annotation
- section: rna_analysis

Many more operations are available. For instance, panels can be filtered by individual tool IDs or regular expressions matching tool IDs. So if one wants to discourage the use of Bowtie and TopHat in favor of HiSat, and might want to disable mappers that come bundled with Galaxy in this view, this can be done by using the excludes directive on a section definition or reference.

- section: mapping
  excludes:
  - tool_id_regex: '.*bowtie.*'
  - tool_id_regex: '.*tophat.*'
  - tool_id: 'bfast_wrapper'
  - tool_id: 'srma_wrapper'
  - tool_id: 'PerM'

It’s possible to combine multiple sections into a new section - e.g. creating a “Mass Spec” section from proteomics and metabolomics sections in the original integrated tool panel. This can be done with the items_from directive and a new explicit section definition as shown next.

- id: mass-spec
  name: "Mass Spec"
  type: section
  items:
  - items_from: proteomics
  - items_from: metabolomics
  excludes:
  - tool_id_regex: '.*maxquant.*'
  - types: [label]

Notice this can also be filtered the same way. Here we’re also removing all the labels from the original sections and the max quant tool.

One can also just use tools, workflows, labels, and sections to create a whole new tool panel without referencing the original sections at all.

name: Custom Panel Filter
type: generic
items:
- type: label
  text: The Start
- type: tool
  id: empty_list
- type: section
  id: my-section
  name: My Custom Section
  items:
  - type: tool
    id: count_list