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comparison build/tools/SetGprs/SetGprs.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_SetGprs" name="SetGprs" version="2.0.0"> 2 <tool id="met4j_SetGprs" name="SetGprs" version="2.0.1">
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: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.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>
51
51 <param name="sbml" value="toy_model.xml"/> 52 <param name="sbml" value="toy_model.xml"/>
53
52 <param name="tab" value="gpr.tsv"/> 54 <param name="tab" value="gpr.tsv"/>
55
53 <output ftype="sbml" name="out"> 56 <output ftype="sbml" name="out">
57
54 <assert_contents> 58 <assert_contents>
59
55 <is_valid_xml/> 60 <is_valid_xml/>
61
56 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> 62 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
63
57 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> 64 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
65
58 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> 66 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/>
67
59 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> 68 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/>
69
60 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> 70 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/>
71
61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> 72 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
73
62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> 74 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
75
63 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> 76 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/>
77
64 <has_line_matching expression=".*fbc:and.*" n="2"/> 78 <has_line_matching expression=".*fbc:and.*" n="2"/>
79
65 </assert_contents> 80 </assert_contents>
81
66 </output> 82 </output>
83
67 </test> 84 </test>
68 </tests> 85 </tests>
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 86 <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
70 The ids must correspond between the tabulated file and the SBML file. 87 The ids must correspond between the tabulated file and the SBML file.
71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 88 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.