<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0">
  <description>Create a Meta-Network from two sub-networks in SBML format.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
 -n2 "$sbml2FilePath"
 -n1ex "$external1"
 -n2ex "$external2"
#if str($n1prefix):
 -n1px "$n1prefix"
#end if
#if str($n2prefix):
 -n2px "$n2prefix"
#end if
 $keepCompartment
 $firstIsMeta
#if str($mergingCriterion):
 -mc "$mergingCriterion"
#end if
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-n1" format="sbml" label="input SBML file: path to first network, in sbml format." name="sbml1FilePath" optional="false" type="data" value=""/>
    <param argument="-n2" format="" label="input SBML file: path to second network, in sbml format." name="sbml2FilePath" optional="false" type="data" value=""/>
    <param argument="-n1ex" label="external compartment identifier in first network." name="external1" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-n2ex" label="external compartment identifier in second network." name="external2" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-n1px" label="prefix that will be added to first network's entities identifiers" name="n1prefix" optional="true" type="text" value="Net1_">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-n2px" label="prefix that will be added to second network's entities identifiers" name="n2prefix" optional="true" type="text" value="Net2_">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-k" checked="false" falsevalue="" label="keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment" name="keepCompartment" truevalue="-k" type="boolean" value="false"/>
    <param argument="-n1meta" checked="false" falsevalue="" label="treat first network as meta-network, allowing more than two sub-models with iterative fusions. This will overwrite shared compartment and pool compounds (which must follow the &quot;pool_&quot; prefix convention) and will ignore --n1prefix argument" name="firstIsMeta" truevalue="-n1meta" type="boolean" value="false"/>
    <param argument="-mc" label="field used to identify the same metabolites across the two different networks. &quot;by_name&quot;/&quot;by_id&quot; can be used if names/identifiers are consistent and unambiguous across source models, &quot;by_metanetx&quot; can be used if models contains MetaNetX identifiers in annotation field using standard miriam format." name="mergingCriterion" optional="true" type="select" value="by_name">
      <option value="by_metanetx">by_metanetx</option>
      <option selected="true" value="by_name">by_name</option>
      <option value="by_id">by_id</option>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
      <param name="sbml2FilePath" value="ECOL.xml"/>
      <param name="external1" value="s"/>
      <param name="external2" value="e"/>
      <param name="n1prefix" value="hsa"/>
      <param name="n2prefix" value="eco"/>
      <param name="mergingCriterion" value="by_metanetx"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help>
  <citations/>
</tool>