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comparison tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.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_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.11.0"> 2 <tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.12.0">
3 <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> 3 <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</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.SbmlSetChargesFromFile#if str($colcharge) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
11 -cc "$colcharge" 11 -cc "$colcharge"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file. 113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
114 If prefix or suffix is different in the SBML file, use the -p or the -s options. 114 If prefix or suffix is different in the SBML file, use the -p or the -s options.
115 The charge will be written in the SBML file in two locations:+ 115 The charge will be written in the SBML file in two locations:+
116 - in the reaction notes (e.g. <p>charge: -1</p>) 116 - in the reaction notes (e.g. <p>charge: -1</p>)
117 - as fbc attribute (e.g. fbc:charge="1")]]></help> 117 - as fbc attribute (e.g. fbc:charge="1")]]></help>
118 <citations/>
118 </tool> 119 </tool>