<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SBMLwizard" name="SBMLwizard" version="1.5.0">
  <description>General SBML model processing</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath"
#if str($inputSide) != 'None':
 -rc "$inputSide"
#end if
 $removeIsolated
#if str($inputReactions) != 'None':
 -rr "$inputReactions"
#end if
 $removeNoFlux
#if str($mergingStrat):
 -mc "$mergingStrat"
#end if
 $removeDuplicated
#if str($exchangeCompToRemove):
 -rEX "$exchangeCompToRemove"
#end if
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/>
    <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
    <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/>
    <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/>
    <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. &quot;by_name&quot; can be used if names are consistent and unambiguous across compartments, &quot;by_id&quot; can be used if compartment suffix is present in compounds identifiers (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
      <option selected="true" value="no">no</option>
      <option value="by_name">by_name</option>
      <option value="by_id">by_id</option>
    </param>
    <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
    <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="removeIsolated" value="true"/>
      <param name="removeNoFlux" value="true"/>
      <param name="mergingStrat" value="by_id"/>
      <param name="removeDuplicated" value="true"/>
      <param name="exchangeCompToRemove" value="s"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="removeIsolated" value="true"/>
      <param name="removeNoFlux" value="true"/>
      <param name="removeDuplicated" value="true"/>
      <param name="inputSide" value="XF_network_C_Side.tab"/>
      <param name="inputReactions" value="XF_network_R_Seed.tab"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
  <citations/>
</tool>