<tool id="preparecommet" name="Prepare commet" version="1.0">
  <description>input sets file</description>
<command interpreter="python">
prepare_commet.py
${read_sets}
#for $set in $sets
    ${set.reads}
    "${set.setname}"
#end for

</command>

  <inputs>
	<!-- Input data files -->
	<repeat name="sets" title="Read sets" min="1">
	    <param name="reads" type="data" multiple="true" format="fasta, fasta.gz, fastq, fastq.gz" label="Dataset"/>
	    <param name="setname" type="text" label="Set name" value="set_name"/>
	</repeat>
  </inputs>

  <outputs>
      <data format="commet" name="read_sets" label="read_sets : ${tool.name} on ${on_string}" />
  </outputs>
  <help>

**Description**

Prepare a configuration file with sets for commet tool 

-------

**Created and integrated by**

Yvan Le Bras and Cyril Monjeaud 

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)

support@genouest.org

If you use this tool in Galaxy, please cite :

`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_

  </help>

<citations>
<citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
    author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
    title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
    booktitle = {JOBIM 2013 Proceedings},
    year = {2013},
    url = {https://www.e-biogenouest.org/resources/128},
    pages = {97-106}
    }
</citation>
</citations>

</tool>