galaxyRPreader.xml

<tool id="rpRankerReader" name="RP reader" version="1.0">
  <description>Convert the output of RP2paths to SBML files</description>
  <requirements>
    <container type="docker">ibisba/rpranker:latest</container>
  </requirements>
  <!--
  <stdio>
    <exit_code range="1:" level="error"/>
  </stdio>
  -->
  <stdio>
		<regex match="WARNING:" level="warning" />
	</stdio>
  <command><![CDATA[
    '$__tool_directory__/wrapRPreader.py' -rp2paths_compounds '$rp2paths_compounds' -rp2paths_scope '$rp2paths_scope' -rp2paths_outPaths '$rp2paths_outPaths' -outSBMLzip '$outSBMLzip'
  ]]></command>
  <inputs>
    <param name="rp2paths_outPaths" type="data" format="csv" label="RP2paths out_paths" />
    <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounts" />
    <param name="rp2paths_scope" type="data" format="csv" label="RP2paths scope results" />
  </inputs>
  <outputs>
    <data name="outSBMLzip" format="zip" label="rpSBML" />
  </outputs>
  <help>
    Parse the rp2paths output to the 
  </help>
</tool>

<!--      
    <data name="outSBMLtar" format="tar.xz" label="rpSBML" />
    '$__tool_directory__/wrapRPreader.py' -rp2paths_compounds '$rp2paths_compounds' -rp2paths_scope '$rp2paths_scope' -model_compartments '$model_compartments' -model_sink '$model_sink' -rp2paths_outPaths '$rp2paths_outPaths' -outSBMLtar '$outSBMLtar'

    <param name="model_compartments" type="data" format="tsv" label="Model list of compartments" />
    <param name="model_sink" type="data" format="tsv" label="Model list of chemicals (RP sink)" />
 -->