Mercurial > repos > metexplore > met4j
annotate build/tools/ExtractPathways/ExtractPathways.xml @ 7:1436e9cde9c9 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author | metexplore |
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date | Tue, 04 Jul 2023 10:21:26 +0000 |
parents | 7a6f2380fc1d |
children | 1274e2a62479 |
rev | line source |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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1 <?xml version="1.0" encoding="UTF-8"?> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.4.0"> |
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3 <description>Extract pathway(s) from GSMN</description> |
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4 <xrefs> |
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5 <xref type="bio.tools">met4j</xref> |
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6 </xrefs> |
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7 <requirements> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> |
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9 </requirements> |
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath" |
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11 -p "$pathwayId" |
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12 -o "$outputPath" |
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13 ]]></command> |
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14 <inputs> |
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15 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> |
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16 <param argument="-p" label="pathway identifiers, separated by "+" sign if more than one" name="pathwayId" optional="false" type="text" value=""> |
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17 <sanitizer invalid_char="_"> |
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18 <valid initial="string.printable"/> |
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19 </sanitizer> |
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20 </param> |
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21 </inputs> |
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22 <outputs> |
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23 <data format="sbml" name="outputPath"/> |
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24 </outputs> |
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25 <tests> |
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26 <test> |
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27 <param name="inputPath" value="XF_network.sbml"/> |
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28 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/> |
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29 <output ftype="sbml" name="outputPath"> |
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30 <assert_contents> |
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31 <is_valid_xml/> |
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32 <has_line_matching expression=".*<reaction.*" n="17"/> |
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33 <has_line_matching expression=".*groups:id=.*" n="2"/> |
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34 </assert_contents> |
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35 </output> |
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36 </test> |
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37 </tests> |
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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> |
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39 <citations/> |
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40 </tool> |