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comparison build/tools/SetChemicalFormulas/SetChemicalFormulas.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_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.0"> 2 <tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.1">
3 <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> 3 <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</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.SetChemicalFormulas#if str($colformula) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan':
11 -cf "$colformula" 11 -cf "$colformula"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
48 <outputs> 48 <outputs>
49 <data format="sbml" name="out"/> 49 <data format="sbml" name="out"/>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53
53 <param name="sbml" value="toy_model.xml"/> 54 <param name="sbml" value="toy_model.xml"/>
55
54 <param name="tab" value="formula.tsv"/> 56 <param name="tab" value="formula.tsv"/>
57
55 <output ftype="sbml" name="out"> 58 <output ftype="sbml" name="out">
59
56 <assert_contents> 60 <assert_contents>
61
57 <is_valid_xml/> 62 <is_valid_xml/>
63
58 <has_line_matching expression=".*CH6O6.*" n="2"/> 64 <has_line_matching expression=".*CH6O6.*" n="2"/>
65
59 <has_line_matching expression=".*CH12O4.*" n="2"/> 66 <has_line_matching expression=".*CH12O4.*" n="2"/>
67
60 </assert_contents> 68 </assert_contents>
69
61 </output> 70 </output>
71
62 </test> 72 </test>
63 <test expect_failure="true"> 73 <test expect_failure="true">
74
64 <param name="sbml" value="toy_model.xml"/> 75 <param name="sbml" value="toy_model.xml"/>
76
65 <param name="tab" value="formulaBad.tsv"/> 77 <param name="tab" value="formulaBad.tsv"/>
78
66 </test> 79 </test>
67 </tests> 80 </tests>
68 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas 81 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
69 The ids must correspond between the tabulated file and the SBML file. 82 The ids must correspond between the tabulated file and the SBML file.
70 If prefix or suffix is different in the SBML file, use the -p or the -s options. 83 If prefix or suffix is different in the SBML file, use the -p or the -s options.