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comparison build/tools/SetReferences/SetReferences.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
comparison
equal deleted inserted replaced
9:0976a6257300 10:6a112eaf8f38
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="develop"> 2 <tool id="met4j_SetReferences" name="SetReferences" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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>
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77 <param name="sbml" value="toy_model.xml"/> 71 <param name="sbml" value="toy_model.xml"/>
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84 <param name="tab" value="refs.tsv"/> 72 <param name="tab" value="refs.tsv"/>
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91 <param name="ref" value="InChi"/> 73 <param name="ref" value="InChi"/>
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98 <param name="o" value="METABOLITE"/> 74 <param name="o" value="METABOLITE"/>
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105 <output ftype="sbml" name="out"> 75 <output ftype="sbml" name="out">
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112 <assert_contents> 76 <assert_contents>
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119 <is_valid_xml/> 77 <is_valid_xml/>
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126 <has_line_matching expression=".*C2H6O.*" n="3"/> 78 <has_line_matching expression=".*C2H6O.*" n="3"/>
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133 <has_line_matching expression=".*C6H8O6.*" n="1"/> 79 <has_line_matching expression=".*C6H8O6.*" n="1"/>
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140 </assert_contents> 80 </assert_contents>
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147 </output> 81 </output>
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154 </test> 82 </test>
155 </tests> 83 </tests>
156 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references 84 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
157 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry) 85 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
158 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help> 86 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help>