comparison tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.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_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.11.0">
  <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</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.SbmlSetEcsFromFile#if str($colec) != 'nan':
 -cec "$colec"
#end if
#if str($colid) != 'nan':

    </test>
  </tests>
  <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC
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.
The EC will be written in the SBML file in two locations:+
- in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>)
- as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help>
</tool>

1:9b162ee6ff8e

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.12.0">
  <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</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.SbmlSetEcsFromFile#if str($colec) != 'nan':
 -cec "$colec"
#end if
#if str($colid) != 'nan':

    </test>
  </tests>
  <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC
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.
The EC will be written in the SBML file in two locations:
- in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>)
- as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help>
  <citations/>
</tool>