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comparison tools/attributes/ExtractPathways/ExtractPathways.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="develop">
3 <description>Extract pathway(s) from GSMN</description> 3 <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath"
11 -p "$pathwayId" 11 -p "$pathwayId"
12 -o "$outputPath" 12 -o "$outputPath"
13 ]]></command> 13 ]]></command>
22 <outputs> 22 <outputs>
23 <data format="sbml" name="outputPath"/> 23 <data format="sbml" name="outputPath"/>
24 </outputs> 24 </outputs>
25 <tests> 25 <tests>
26 <test> 26 <test>
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27 <param name="inputPath" value="XF_network.sbml"/> 38 <param name="inputPath" value="XF_network.sbml"/>
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28 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> 50 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
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29 <output ftype="sbml" name="outputPath"> 62 <output ftype="sbml" name="outputPath">
30 <assert_contents> 63
31 <is_valid_xml/> 64
32 <has_line_matching expression=".*&lt;reaction.*" n="17"/> 65
33 <has_line_matching expression=".*groups:id=.*" n="2"/> 66
34 </assert_contents> 67
35 </output> 68
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74 <assert_contents>
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86 <is_valid_xml/>
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98 <has_line_matching expression=".*&lt;reaction.*" n="17"/>
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110 <has_line_matching expression=".*groups:id=.*" n="2"/>
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122 </assert_contents>
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134 </output>
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36 </test> 146 </test>
37 </tests> 147 </tests>
38 <help><![CDATA["Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help> 148 <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help>
39 <citations/> 149 <citations/>
40 </tool> 150 </tool>