comparison SetPathways.xml @ 3:f610e716950a draft default tip

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

2:b76767e37412

    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="pathways.tsv"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*groups:id=.*" n="3"/>
          <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
          <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
          <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="pathwaysOtherSep.tsv"/>
      <param name="sep" value=" + "/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*groups:id=.*" n="3"/>
          <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
          <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
          <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
The ids must correspond between the tabulated file and the SBML file.
If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)
@ATTRIBUTION@]]></help>

3:f610e716950a

    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests/>
  <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
The ids must correspond between the tabulated file and the SBML file.
If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)
@ATTRIBUTION@]]></help>