comparison tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml @ 1:9b162ee6ff8e draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95

0:dcd16521b969

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.11.0">
  <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
 -cp "$colp"
#end if
#if str($sep):

  </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. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
      <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
        <groups:listOfMembers>
          <groups:member groups:idRef="R_GLUPRT"/>
          <groups:member groups:idRef="R_RNDR1b"/>
...
]]></help>
</tool>

1:9b162ee6ff8e

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0">
  <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
 -cp "$colp"
#end if
#if str($sep):

  </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. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
 <groups:listOfMembers>
  <groups:member groups:idRef="R_GLUPRT"/>
  <groups:member groups:idRef="R_RNDR1b"/>
...
]]></help>
  <citations/>
</tool>