<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16">
  <description>To run the CarboSeq simulator</description>
  <environment_variables>
    <environment_variable name="TMPDIR">\$(realpath -s tmp)</environment_variable>
  </environment_variables>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  (env | grep DOCKER_IMAGE) &&
  printf " Image  Reg   : \$s\n" \$(env | grep DOCKER_IMAGE) &&
  bash -e -c "mkdir output &&
  unzip -d input ${input} &&
  cp /usr/local/src/myscripts/semantifier.jar . &&
  cp /usr/local/src/myscripts/start_server.sh . &&
  cp -r /usr/local/src/myscripts/config_mappers . &&
  cp -r /usr/local/src/myscripts/data . &&
  Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
  cp output/* ${output}"
    ]]>
  </command>
  <inputs>
    <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
    <param name="semantifier" type="select" label="Choose the semantifier mode:">
      <option value="modeltoolbox_sem_local" selected="true">local</option>
      <option value="modeltoolbox_sem_remote">remote</option>
    </param>
  </inputs>
  <outputs>
    <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input/40Sites.zip" ftype="zip" />
      <param name="semantifier" value="modeltoolbox_sem_local" />
      <output name="output" ftype="rdata" >
      	<assert_contents>
	  <has_size value="1202" negate="false" />
	  <has_size value="0" negate="true" />
	</assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="input/40Sites.zip" ftype="zip" />
      <param name="semantifier" value="modeltoolbox_sem_remote" />
      <output name="output" ftype="rdata" >
      	<assert_contents>
	  <has_size value="1202" negate="false" />
	  <has_size value="0" negate="true" />
	</assert_contents>
      </output>
    </test>
  </tests>
  <help>
the CarboSeq CarboseqSimulator tool
===================================

credits
-------
-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
-  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
-  Copyright: INRAE
</help>
</tool>