Implementing Galaxy tool.

Implementing a Galaxy tool

Introduction

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

Eoulsan can interpret a galaxytools XML file to create a step in a workflow. For more information about galaxy tools: The Galaxy Project website

Galaxy tools tags

The following code defines an XML example for Galaxy in Eoulsan:

<tool id="bam2bedgraph" name="bam2bedgraph">
  <description>Convert bam files to bigwig file</description>
  <command>bamCoverage -b $input_bam -bai $input_bai -o $output_bedgraph -of bedgraph</command>
  <inputs>
    <param format="bam" name="input_bam" type="data" label="Source file"/>
    <param format="bai" name="input_bai" type="data" label="Source file"/>
  </inputs>
  <outputs>
    <data format="bedgraph" name="output_bedgraph" />
  </outputs>

</tool>

Here is a list of the supported galaxy tools tags by eoulsan:

• <tool> tag, has two mandatory elements id and name, which are necessary for eoulsan.
• <description> tag obviously contains the tool's description.
• <command> tag contains the command line of the tool you want to use.
• <inputs> tag contains param tags, defining the input files for the galaxy step.
• for each<param> tag in inputs tag, you can define an input file
• <outputs> tag contains data tags, defining the output files of the galaxy step.
• for each <data> tag in outputs tag, you can define an output file
• <conditional> tag is a container for conditional parameters (must contain <when> tag and command line is then wrapped in an if-else statement).

Limitations

Eoulsan currently only supports the previously defined tags from galaxy tools XML files.

dataformat also need to be defined. See the Eoulsan dataformat wiki section for more informations.

Galaxy tools using a Docker image

Eoulsan also implements additional function to manage docker images. You can execute a command through an available docker image, using interpreter="docker" and dockerimage elements in command tag. When you use Docker as interpreter, you can also define a fallback interpreter if Docker is not installed on the system (e.g. interpreter="docker,bash").

Here is an example:

<command interpreter="docker,bash" dockerimage="genomicpariscentre/deeptools:1.5.12">
   bamCoverage -b $input_bam -bai $input_bai -o $output_bedgraph -of bedgraph
</command>

It is also possible to launch the value of the command tag as a command when Docker isn't available (ie, interpreter="docker,").

Files locations

The location of galaxy tools and formats XML files need to be specified to Eoulsan.

Either add to .eoulsan file in your home folder:

main.format.path=/home/firmo/tests/galaxy/eoulsan-tools/formats
main.galaxy.tool.path=/home/firmo/tests/galaxy/eoulsan-tools/galaxytools

An alternative, in the workflow.xml file

        <parameter>
	        <name>main.galaxy.tool.path</name>
	        <value>/home/firmo/tests/galaxy/eoulsan-tools/galaxytools</value>
        </parameter>
        <parameter>
	        <name>main.format.path</name>
	        <value>/home/firmo/tests/galaxy/eoulsan-tools/formats</value>
        </parameter>

Note: Those parameter can even be a link to a repository.

Here is an example:

main.format.path=https://raw.githubusercontent.com/GenomicParisCentre/eoulsan-tools/master/formats
main.galaxy.tool.path=https://raw.githubusercontent.com/GenomicParisCentre/eoulsan-tools/master/galaxytools