Mercurial > repos > metexplore > met4j_extractpathways
comparison ExtractPathways.xml @ 0:effdd70905ed draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
| author | metexplore |
|---|---|
| date | Thu, 13 Mar 2025 15:42:11 +0000 |
| parents | |
| children | 03a77f9c808d |
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| -1:000000000000 | 0:effdd70905ed |
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| 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> | |
| 2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="@TOOL_VERSION@"> | |
| 3 <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="bio_tools"/> | |
| 8 <expand macro="requirements"/> | |
| 9 <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.attributes.ExtractPathways -i "$inputPath" | |
| 10 -p "$pathwayId" | |
| 11 -o "$outputPath" | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | |
| 15 <param argument="-p" label="pathway identifiers, separated by "+" sign if more than one" name="pathwayId" optional="false" type="text" value=""> | |
| 16 <sanitizer invalid_char="_"> | |
| 17 <valid initial="string.printable"/> | |
| 18 </sanitizer> | |
| 19 </param> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="sbml" name="outputPath"/> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="inputPath" value="XF_network.sbml"/> | |
| 27 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> | |
| 28 <output ftype="sbml" name="outputPath"> | |
| 29 <assert_contents> | |
| 30 <is_valid_xml/> | |
| 31 <has_line_matching expression=".*<reaction.*" n="17"/> | |
| 32 <has_line_matching expression=".*groups:id=.*" n="2"/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file | |
| 38 @ATTRIBUTION@]]></help> | |
| 39 <citations/> | |
| 40 </tool> |