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comparison build/tools/SetChemicalFormulas/SetChemicalFormulas.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_SetChemicalFormulas" name="SetChemicalFormulas" version="develop"> 2 <tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.0">
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: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.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>
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59 <param name="sbml" value="toy_model.xml"/> 53 <param name="sbml" value="toy_model.xml"/>
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66 <param name="tab" value="formula.tsv"/> 54 <param name="tab" value="formula.tsv"/>
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73 <output ftype="sbml" name="out"> 55 <output ftype="sbml" name="out">
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80 <assert_contents> 56 <assert_contents>
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87 <is_valid_xml/> 57 <is_valid_xml/>
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94 <has_line_matching expression=".*CH6O6.*" n="2"/> 58 <has_line_matching expression=".*CH6O6.*" n="2"/>
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101 <has_line_matching expression=".*CH12O4.*" n="2"/> 59 <has_line_matching expression=".*CH12O4.*" n="2"/>
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108 </assert_contents> 60 </assert_contents>
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115 </output> 61 </output>
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122 </test> 62 </test>
123 <test expect_failure="true"> 63 <test expect_failure="true">
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130 <param name="sbml" value="toy_model.xml"/> 64 <param name="sbml" value="toy_model.xml"/>
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137 <param name="tab" value="formulaBad.tsv"/> 65 <param name="tab" value="formulaBad.tsv"/>
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144 </test> 66 </test>
145 </tests> 67 </tests>
146 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas 68 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
147 The ids must correspond between the tabulated file and the SBML file. 69 The ids must correspond between the tabulated file and the SBML file.
148 If prefix or suffix is different in the SBML file, use the -p or the -s options. 70 If prefix or suffix is different in the SBML file, use the -p or the -s options.