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comparison tools/attributes/SetReferences/SetReferences.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
comparison
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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_SetReferences" name="SetReferences" version="2.0.0"> 2 <tool id="met4j_SetReferences" name="SetReferences" version="2.0.1">
3 <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</description> 3 <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</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.SetReferences#if str($colRef) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan':
11 -cr "$colRef" 11 -cr "$colRef"
12 #end if 12 #end if
13 -ref "$ref" 13 -ref "$ref"
66 <outputs> 66 <outputs>
67 <data format="sbml" name="out"/> 67 <data format="sbml" name="out"/>
68 </outputs> 68 </outputs>
69 <tests> 69 <tests>
70 <test> 70 <test>
71
71 <param name="sbml" value="toy_model.xml"/> 72 <param name="sbml" value="toy_model.xml"/>
73
72 <param name="tab" value="refs.tsv"/> 74 <param name="tab" value="refs.tsv"/>
75
73 <param name="ref" value="InChi"/> 76 <param name="ref" value="InChi"/>
77
74 <param name="o" value="METABOLITE"/> 78 <param name="o" value="METABOLITE"/>
79
75 <output ftype="sbml" name="out"> 80 <output ftype="sbml" name="out">
81
76 <assert_contents> 82 <assert_contents>
83
77 <is_valid_xml/> 84 <is_valid_xml/>
85
78 <has_line_matching expression=".*C2H6O.*" n="3"/> 86 <has_line_matching expression=".*C2H6O.*" n="3"/>
87
79 <has_line_matching expression=".*C6H8O6.*" n="1"/> 88 <has_line_matching expression=".*C6H8O6.*" n="1"/>
89
80 </assert_contents> 90 </assert_contents>
91
81 </output> 92 </output>
93
82 </test> 94 </test>
83 </tests> 95 </tests>
84 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references 96 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
85 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry) 97 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
86 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help> 98 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help>