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comparison build/tools/SetGprs/SetGprs.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_SetGprs" name="SetGprs" version="develop"> 2 <tool id="met4j_SetGprs" name="SetGprs" version="2.0.0">
3 <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description> 3 <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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.SetGprs#if str($colgpr) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan':
11 -cgpr "$colgpr" 11 -cgpr "$colgpr"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
46 <outputs> 46 <outputs>
47 <data format="sbml" name="out"/> 47 <data format="sbml" name="out"/>
48 </outputs> 48 </outputs>
49 <tests> 49 <tests>
50 <test> 50 <test>
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57 <param name="sbml" value="toy_model.xml"/> 51 <param name="sbml" value="toy_model.xml"/>
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64 <param name="tab" value="gpr.tsv"/> 52 <param name="tab" value="gpr.tsv"/>
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71 <output ftype="sbml" name="out"> 53 <output ftype="sbml" name="out">
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78 <assert_contents> 54 <assert_contents>
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85 <is_valid_xml/> 55 <is_valid_xml/>
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92 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> 56 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
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99 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> 57 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
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106 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> 58 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/>
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113 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> 59 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/>
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120 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> 60 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/>
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127 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> 61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
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134 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> 62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
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141 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> 63 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/>
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148 <has_line_matching expression=".*fbc:and.*" n="2"/> 64 <has_line_matching expression=".*fbc:and.*" n="2"/>
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155 </assert_contents> 65 </assert_contents>
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162 </output> 66 </output>
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169 </test> 67 </test>
170 </tests> 68 </tests>
171 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way 69 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way
172 The ids must correspond between the tabulated file and the SBML file. 70 The ids must correspond between the tabulated file and the SBML file.
173 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.