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comparison tools/attributes/ExtractPathways/ExtractPathways.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
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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_ExtractPathways" name="ExtractPathways" version="2.0.0"> 2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="2.0.1">
3 <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</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: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.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>
27
27 <param name="inputPath" value="XF_network.sbml"/> 28 <param name="inputPath" value="XF_network.sbml"/>
29
28 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> 30 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
31
29 <output ftype="sbml" name="outputPath"> 32 <output ftype="sbml" name="outputPath">
33
30 <assert_contents> 34 <assert_contents>
35
31 <is_valid_xml/> 36 <is_valid_xml/>
37
32 <has_line_matching expression=".*&lt;reaction.*" n="17"/> 38 <has_line_matching expression=".*&lt;reaction.*" n="17"/>
39
33 <has_line_matching expression=".*groups:id=.*" n="2"/> 40 <has_line_matching expression=".*groups:id=.*" n="2"/>
41
34 </assert_contents> 42 </assert_contents>
43
35 </output> 44 </output>
45
36 </test> 46 </test>
37 </tests> 47 </tests>
38 <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help> 48 <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help>
39 <citations/> 49 <citations/>
40 </tool> 50 </tool>