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comparison tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.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_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.11.0"> 2 <tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0">
3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description> 3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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.SbmlSetPathwaysFromFile#if str($colp) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
11 -cp "$colp" 11 -cp "$colp"
12 #end if 12 #end if
13 #if str($sep): 13 #if str($sep):
85 </tests> 85 </tests>
86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways 86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
87 The ids must correspond between the tabulated file and the SBML file. 87 The ids must correspond between the tabulated file and the SBML file.
88 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 88 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
89 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group: 89 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
90 <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis"> 90 <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
91 <groups:listOfMembers> 91 <groups:listOfMembers>
92 <groups:member groups:idRef="R_GLUPRT"/> 92 <groups:member groups:idRef="R_GLUPRT"/>
93 <groups:member groups:idRef="R_RNDR1b"/> 93 <groups:member groups:idRef="R_RNDR1b"/>
94 ... 94 ...
95 ]]></help> 95 ]]></help>
96 <citations/>
96 </tool> 97 </tool>