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comparison tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.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_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.11.0"> 2 <tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.12.0">
3 <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> 3 <description>Set Formula 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.SbmlSetFormulasFromFile#if str($colformula) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
11 -cf "$colformula" 11 -cf "$colformula"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
70 If prefix or suffix is different in the SBML file, use the -p or the -s options. 70 If prefix or suffix is different in the SBML file, use the -p or the -s options.
71 The formula will be written in the SBML file in two locations:+ 71 The formula will be written in the SBML file in two locations:+
72 - in the metabolite notes (e.g. <p>formula: C16H29O2</p> 72 - in the metabolite notes (e.g. <p>formula: C16H29O2</p>
73 73
74 - as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help> 74 - as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help>
75 <citations/>
75 </tool> 76 </tool>