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comparison tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.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_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.11.0"> 2 <tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.12.0">
3 <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</description> 3 <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</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.SbmlSetEcsFromFile#if str($colec) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
11 -cec "$colec" 11 -cec "$colec"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
64 </test> 64 </test>
65 </tests> 65 </tests>
66 <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC 66 <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC
67 The ids must correspond between the tabulated file and the SBML file. 67 The ids must correspond between the tabulated file and the SBML file.
68 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 68 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
69 The EC will be written in the SBML file in two locations:+ 69 The EC will be written in the SBML file in two locations:
70 - in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>) 70 - in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>)
71 - as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help> 71 - as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help>
72 <citations/>
72 </tool> 73 </tool>