view build/tools/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml @ 7:1436e9cde9c9 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
parents 7a6f2380fc1d
children 1274e2a62479
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<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.4.0">
  <description>Set names to network objects from a tabulated file containing the object ids and the names</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
 -cname "$colname"
#end if
#if str($colid):
 -ci "$colid"
#end if
 $p
 $s
#if str($o):
 -o "$o"
#end if
#if str($nSkip):
 -n "$nSkip"
#end if
 -sbml "$sbml"
#if str($tab) != 'None':
 -tab "$tab"
#end if
#if str($c):
 -c "$c"
#end if
 -out "$out"
]]></command>
  <inputs>
    <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>
    <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
    <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
    <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
    <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="namesMetabolites.tsv"/>
      <param name="o" value="METABOLITE"/>
      <output ftype="sbml" name="out">
      <assert_contents>
        <is_valid_xml/>
        <has_line_matching expression=".*metaboliteA.*" n="1"/>
        <has_line_matching expression=".*metaboliteB.*" n="1"/>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="namesReactions.tsv"/>
      <output ftype="sbml" name="out">
      <assert_contents>
        <is_valid_xml/>
        <has_line_matching expression=".*reaction1.*" n="1"/>
        <has_line_matching expression=".*reaction2.*" n="1"/>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="namesPathways.tsv"/>
      <param name="o" value="PATHWAY"/>
      <output ftype="sbml" name="out">
      <assert_contents>
        <is_valid_xml/>
        <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
        <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="namesGenes.tsv"/>
      <param name="o" value="GENE"/>
      <output ftype="sbml" name="out">
      <assert_contents>
        <is_valid_xml/>
        <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
        <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
      </assert_contents>
    </output>
    </test>
  </tests>
  <help><![CDATA[Set names to network objects from a tabulated file containing the object ids and the names
The ids must correspond between the tabulated file and the SBML file.
If prefix or suffix is different in the SBML file, use the -p or the -s options.
]]></help>
  <citations/>
</tool>