annotate SetNames.xml @ 2:0c353826af4a draft default tip

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetNames" name="SetNames" version="@TOOL_VERSION@">
  <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j attributes.SetNames#if str($colname) != 'nan':
 -cname "$colname"
#end if
#if str($colid):
 -ci "$colid"
#end if
 $p
 $s
#if str($o):
 -t "$o"
#end if
#if str($nSkip):
 -n "$nSkip"
#end if
 -i "$sbml"
#if str($tab) != 'None':
 -tab "$tab"
#end if
#if str($c):
 -c "$c"
#end if
 -o "$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="-t" 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="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-tab" format="tsv" label="Input 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 in a SBML file 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.
@ATTRIBUTION@]]></help>
  <citations/>
</tool>