<tool id="inSiliCow" name="inSiliCow" version="1.0.4">
  <description>to run the inSiliCow simulator</description>
  <requirements>
    <container type="singularity">docker://registry.forge.inrae.fr/insilicow/insilicow-container:a773b01f824979b9f8fef89e89dbda0d7ef04ecb</container>
  </requirements>
  <command detect_errors="aggressive">
    <![CDATA[
	     echo "=================" &&
	     env &&
	     echo "=================" &&
	     cp -r /insilicow-simulator . &&
	     cd insilicow-simulator/scripts &&
	     unzip -d tmp ${in} &&
	     configDir=\$(ls -1 tmp) &&
	     find examples/* -type d | xargs rm -R &&
	     mv -f tmp/* examples &&
	     pwd && ls && echo \$configDir &&
	     head -n -3 ./inSiliCow-run.sh > tmpFile &&
	     mv tmpFile ./inSiliCow-run.sh &&
	     chmod u+x ./inSiliCow-run.sh &&
	     TERM="xterm-256color" ./inSiliCow-run.sh \$configDir &&
	     cd out &&
	     zip -r j* * &&
	     mv *.zip ${out}
     ]]>
  </command>
  <inputs>
    <param name="in" type="data" format="zip" label="Select a inSiliCow config folder (zip file)"/>
  </inputs>
  <outputs>
    <data format="zip" name="out"
          label="inSiliCowOutputs">
    </data>
  </outputs>
  <tests>
    <test>
      <param name="in" value="input/example_00.zip" ftype="zip" />
      <output name="out" ftype="zip" >
	<assert_contents>
	  <has_archive_member path=".*/out/farmer.sh">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path=".*/in/explan.txt">
	    <has_size value="0" negate="true" />
	    <has_text text="end_year" />
	    <has_text text="1971" />
	  </has_archive_member>
	  <has_archive_member path=".*/out/sim_1/events.sqlite">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path=".*/out/sim_1/states.txt">
	    <has_size value="0" negate="true" />
	    <has_text text="CALF" />
	  </has_archive_member>
	  <has_archive_member path=".*/out/sim_1/cows/nb_cows.txt">
	    <has_text text="126" />
	  </has_archive_member>
	</assert_contents>	  
      </output>
    </test>
  </tests>
  <help>
*The usage of this tool is restricted to the user of the insilicow Galaxy/SIWAA group.*

*To be granted, apply to the insilicow Project Team and then request to SIWAA*

Documentation
-------------
A tool to launch the inSiliCow dairy cow herd simulator

Credits
-------
-  Wrappedt tool authors: Olivier Martin (MoSAR) &lt;olivier.martin-mosar@inrae.fr&gt;, Pierre Blavy &lt;pierre.blavy@inrae.fr&gt;
-  Insilicow project site: https://digitbio.hub.inrae.fr/rubriques-verticales2/nos-actions/projets-phares/projet-phare-insilicow-2024-2028
-  Insilicow repository: https://forge.inrae.fr/insilicow
-  Underlying container maintainer: Eric Casellas &lt;eric.casellas@inrae.fr&gt;
-  Galaxy tool maintainer: Patrick Chabrier &lt;patrick.chabrier@inrae.fr&gt;
-  Copyright: INRAE
  </help>
</tool>