Mercurial > repos > metexplore > met4j
comparison tools/attributes/ExtractPathways/ExtractPathways.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
| parents | |
| children | 9b162ee6ff8e |
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| -1:000000000000 | 0:dcd16521b969 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.11.0"> | |
| 3 <description>Extract pathway(s) from GSMN</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" | |
| 11 -p "$pathwayId" | |
| 12 -o "$outputPath" | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | |
| 16 <param argument="-p" label="pathway identifiers, separated by "+" sign if more than one" name="pathwayId" optional="false" type="text" value=""> | |
| 17 <sanitizer invalid_char="_"> | |
| 18 <valid initial="string.printable"/> | |
| 19 </sanitizer> | |
| 20 </param> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="sbml" name="outputPath"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="inputPath" value="XF_network.sbml"/> | |
| 28 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> | |
| 29 <output ftype="sbml" name="outputPath"> | |
| 30 <assert_contents> | |
| 31 <is_valid_xml/> | |
| 32 <has_line_matching expression=".*<reaction.*" n="17"/> | |
| 33 <has_line_matching expression=".*groups:id=.*" n="2"/> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 </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> | |
| 39 </tool> |