Tool Panel Administration¶
The Galaxy tool panel is located on the left of the ‘Analysis page’ and offers the following ways of modification.
The contents of the tool panel are defined by the following configuration files.
Three configuration options define the content of the toolbox:
Built-in and custom tools¶
Built-in tools are defined in the file
is loaded by default. This is because of the default value of the
tool_config_file configuration setting in the
tool_conf.xml (Galaxy loads the sample file
tool_conf.xml is absent).
Further custom tool config files can be listed in
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
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:
A section containing built-in converters can be added to the tool panel
by enabling the
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_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
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.
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
configuration file. The
migrated_tools_conf.xml file is always parsed and
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
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
file as described above.
Tool conf XML syntax¶
A tool configuration file is an XML file containing mainly four elements:
toolboxis the root tag. It has two optional attributes:
tool_pathis used to set the path (relative to Galaxy’s root dir) containing the tools.
monitoris a boolean that indicates if Galaxy should monitor changes to the file.
sectiondefines a section in the tool panel. It needs to have an
idattribute which should have no spaces, and has an optional
nameattribute which defines the text shown to the user (otherwise
labeladds a header line to the tool panel. It needs to have an
idattribute and optionally define a
textattribute which gives the text shown to the user.
tooldefines a tool.
fileattribute gives the path to the tool XML file (relative to the
tool_pathof the toolbox).
labelsrender a label next to the tool in the tool panel, e.g.
guidattribute is set by Galaxy for tools installed from a ToolShed.
label tags are used as child of
tools are used as child of
section. In the following two examples are shown.
<label id="general_text_label" text="General Text Tools" />
<section id="getext" name="Get Data">
<tool file="data_source/upload.xml" />
<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/220.127.116.11">
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
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
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
- 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
excludes directive on a section definition or reference.
- section: mapping
- 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"
- items_from: proteomics
- items_from: metabolomics
- 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: label
text: The Start
- type: tool
- type: section
name: My Custom Section
- type: tool