comparison tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.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_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.11.0">
  <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
 -cgpr "$colgpr"
#end if
#if str($colid) != 'nan':

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.
GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
(The GPR will be written in the SBML file in two locations:
- in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
- as fbc gene product association :       <fbc:geneProductAssociation>
          <fbc:or>
            <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
            <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
          </fbc:or>
        </fbc:geneProductAssociation>
]]></help>
</tool>

1:9b162ee6ff8e

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.12.0">
  <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
 -cgpr "$colgpr"
#end if
#if str($colid) != 'nan':

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.
GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
(The GPR will be written in the SBML file in two locations:
- in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
- as fbc gene product association :<fbc:geneProductAssociation>
 <fbc:or>
  <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
  <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
 </fbc:or>
</fbc:geneProductAssociation>
]]></help>
  <citations/>
</tool>