Implementing a Galaxy format

Implementing a Galaxy format

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 step in a pipeline. For more information about galaxy tools: The Galaxy Project website

Furthermore, unknowndataformat need to be defined to Eoulsan.

Galaxy format file

The following code define a xml example for galaxy dataformat file in eoulsan:

<dataformat>
  <name>bigwig_bw</name>
  <description>bigwig format</description>
  <alias>bigwig</alias>
  <prefix>bigwig</prefix>
  <extensions>
  	<extension default="true">.bw</extension>
  </extensions>

  <toolshedgalaxy>
  	<extension>bigwig</extension> 	
  </toolshedgalaxy>
</dataformat>

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

• <dataformat> which is necessary for eoulsan.
• <description> tag obviously contains the format's description.
• <name> tag.
• <extensions> tag contains the extension for the file to be recognized as the dataformat
• <toolshedgalaxy>
• <extension>

Limitations

Eoulsan currently only supports the previously defined tags from galaxy format xml files.

Files locations

To allow Eoulsan to recognize and use the galaxy tool. 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