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

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
author metexplore
date Mon, 27 Jun 2022 13:41:08 +0000
parents dcd16521b969
children e69a78624877
comparison
equal deleted inserted replaced
0:dcd16521b969 1:9b162ee6ff8e
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.11.0"> 2 <tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.12.0">
3 <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> 3 <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>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
11 -cgpr "$colgpr" 11 -cgpr "$colgpr"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
70 The ids must correspond between the tabulated file and the SBML file. 70 The ids must correspond between the tabulated file and the SBML file.
71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
72 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 72 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
73 (The GPR will be written in the SBML file in two locations: 73 (The GPR will be written in the SBML file in two locations:
74 - in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p> 74 - in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
75 - as fbc gene product association : <fbc:geneProductAssociation> 75 - as fbc gene product association :<fbc:geneProductAssociation>
76 <fbc:or> 76 <fbc:or>
77 <fbc:geneProductRef fbc:geneProduct="XC_3282"/> 77 <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
78 <fbc:geneProductRef fbc:geneProduct="XC_0401"/> 78 <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
79 </fbc:or> 79 </fbc:or>
80 </fbc:geneProductAssociation> 80 </fbc:geneProductAssociation>
81 ]]></help> 81 ]]></help>
82 <citations/>
82 </tool> 83 </tool>