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comparison build/tools/SetPathways/SetPathways.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
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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_SetPathways" name="SetPathways" version="develop"> 2 <tool id="met4j_SetPathways" name="SetPathways" version="2.0.0">
3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description> 3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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.SetPathways#if str($colp) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetPathways#if str($colp) != 'nan':
11 -cp "$colp" 11 -cp "$colp"
12 #end if 12 #end if
13 #if str($sep): 13 #if str($sep):
54 <outputs> 54 <outputs>
55 <data format="sbml" name="out"/> 55 <data format="sbml" name="out"/>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>
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65 <param name="sbml" value="toy_model.xml"/> 59 <param name="sbml" value="toy_model.xml"/>
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72 <param name="tab" value="pathways.tsv"/> 60 <param name="tab" value="pathways.tsv"/>
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79 <output ftype="sbml" name="out"> 61 <output ftype="sbml" name="out">
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86 <assert_contents> 62 <assert_contents>
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93 <is_valid_xml/> 63 <is_valid_xml/>
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100 <has_line_matching expression=".*groups:id=.*" n="3"/> 64 <has_line_matching expression=".*groups:id=.*" n="3"/>
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107 <has_line_matching expression=".*groups:id=.p1.*" n="1"/> 65 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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114 <has_line_matching expression=".*groups:id=.p2.*" n="1"/> 66 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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121 <has_line_matching expression=".*groups:id=.p3.*" n="1"/> 67 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
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128 </assert_contents> 68 </assert_contents>
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135 </output> 69 </output>
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142 </test> 70 </test>
143 <test> 71 <test>
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150 <param name="sbml" value="toy_model.xml"/> 72 <param name="sbml" value="toy_model.xml"/>
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157 <param name="tab" value="pathwaysOtherSep.tsv"/> 73 <param name="tab" value="pathwaysOtherSep.tsv"/>
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164 <param name="sep" value=" + "/> 74 <param name="sep" value=" + "/>
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171 <output ftype="sbml" name="out"> 75 <output ftype="sbml" name="out">
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178 <assert_contents> 76 <assert_contents>
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185 <is_valid_xml/> 77 <is_valid_xml/>
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192 <has_line_matching expression=".*groups:id=.*" n="3"/> 78 <has_line_matching expression=".*groups:id=.*" n="3"/>
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199 <has_line_matching expression=".*groups:id=.p1.*" n="1"/> 79 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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206 <has_line_matching expression=".*groups:id=.p2.*" n="1"/> 80 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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213 <has_line_matching expression=".*groups:id=.p3.*" n="1"/> 81 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
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220 </assert_contents> 82 </assert_contents>
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227 </output> 83 </output>
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234 </test> 84 </test>
235 </tests> 85 </tests>
236 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways 86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
237 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.
238 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.