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comparison build/tools/SetPathways/SetPathways.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SetPathways" name="SetPathways" version="2.0.0"> 2 <tool id="met4j_SetPathways" name="SetPathways" version="2.0.1">
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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan':
11 -cp "$colp" 11 -cp "$colp"
12 #end if 12 #end if
13 #if str($sep): 13 #if str($sep):
54 <outputs> 54 <outputs>
55 <data format="sbml" name="out"/> 55 <data format="sbml" name="out"/>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>
59
59 <param name="sbml" value="toy_model.xml"/> 60 <param name="sbml" value="toy_model.xml"/>
61
60 <param name="tab" value="pathways.tsv"/> 62 <param name="tab" value="pathways.tsv"/>
63
61 <output ftype="sbml" name="out"> 64 <output ftype="sbml" name="out">
65
62 <assert_contents> 66 <assert_contents>
67
63 <is_valid_xml/> 68 <is_valid_xml/>
69
64 <has_line_matching expression=".*groups:id=.*" n="3"/> 70 <has_line_matching expression=".*groups:id=.*" n="3"/>
71
65 <has_line_matching expression=".*groups:id=.p1.*" n="1"/> 72 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
73
66 <has_line_matching expression=".*groups:id=.p2.*" n="1"/> 74 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
75
67 <has_line_matching expression=".*groups:id=.p3.*" n="1"/> 76 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
77
68 </assert_contents> 78 </assert_contents>
79
69 </output> 80 </output>
81
70 </test> 82 </test>
71 <test> 83 <test>
84
72 <param name="sbml" value="toy_model.xml"/> 85 <param name="sbml" value="toy_model.xml"/>
86
73 <param name="tab" value="pathwaysOtherSep.tsv"/> 87 <param name="tab" value="pathwaysOtherSep.tsv"/>
88
74 <param name="sep" value=" + "/> 89 <param name="sep" value=" + "/>
90
75 <output ftype="sbml" name="out"> 91 <output ftype="sbml" name="out">
92
76 <assert_contents> 93 <assert_contents>
94
77 <is_valid_xml/> 95 <is_valid_xml/>
96
78 <has_line_matching expression=".*groups:id=.*" n="3"/> 97 <has_line_matching expression=".*groups:id=.*" n="3"/>
98
79 <has_line_matching expression=".*groups:id=.p1.*" n="1"/> 99 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
100
80 <has_line_matching expression=".*groups:id=.p2.*" n="1"/> 101 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
102
81 <has_line_matching expression=".*groups:id=.p3.*" n="1"/> 103 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
104
82 </assert_contents> 105 </assert_contents>
106
83 </output> 107 </output>
108
84 </test> 109 </test>
85 </tests> 110 </tests>
86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways 111 <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. 112 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. 113 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.