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comparison tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml @ 2:e69a78624877 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
author metexplore
date Tue, 19 Jul 2022 14:20:07 +0000
parents 9b162ee6ff8e
children 6bd9aad9626d
comparison
equal deleted inserted replaced
1:9b162ee6ff8e 2:e69a78624877
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0"> 2 <tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.0.1">
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:0.12.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</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):
60 <param name="tab" value="pathways.tsv"/> 60 <param name="tab" value="pathways.tsv"/>
61 <output ftype="sbml" name="out"> 61 <output ftype="sbml" name="out">
62 <assert_contents> 62 <assert_contents>
63 <is_valid_xml/> 63 <is_valid_xml/>
64 <has_line_matching expression=".*groups:id=.*" n="3"/> 64 <has_line_matching expression=".*groups:id=.*" n="3"/>
65 <has_line_matching expression=".*groups:id=.P1.*" n="1"/> 65 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
66 <has_line_matching expression=".*groups:id=.P2.*" n="1"/> 66 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
67 <has_line_matching expression=".*groups:id=.P3.*" n="1"/> 67 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
68 </assert_contents> 68 </assert_contents>
69 </output> 69 </output>
70 </test> 70 </test>
71 <test> 71 <test>
72 <param name="sbml" value="toy_model.xml"/> 72 <param name="sbml" value="toy_model.xml"/>
74 <param name="sep" value=" + "/> 74 <param name="sep" value=" + "/>
75 <output ftype="sbml" name="out"> 75 <output ftype="sbml" name="out">
76 <assert_contents> 76 <assert_contents>
77 <is_valid_xml/> 77 <is_valid_xml/>
78 <has_line_matching expression=".*groups:id=.*" n="3"/> 78 <has_line_matching expression=".*groups:id=.*" n="3"/>
79 <has_line_matching expression=".*groups:id=.P1.*" n="1"/> 79 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
80 <has_line_matching expression=".*groups:id=.P2.*" n="1"/> 80 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
81 <has_line_matching expression=".*groups:id=.P3.*" n="1"/> 81 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
82 </assert_contents> 82 </assert_contents>
83 </output> 83 </output>
84 </test> 84 </test>
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