Mercurial > repos > metexplore > met4j
comparison build/tools/PrecursorNetwork/PrecursorNetwork.xml @ 11:40c15b7467f1 draft default tip
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 |
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| 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> | 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
| 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.0"> | 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.1"> |
| 3 <description>Perform a network expansion from a set of compound targets to create a precursor network.</description> | 3 <description>Perform a network expansion from a set of compound targets to create a precursor network.</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 networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" |
| 11 -t "$targetsFilePath" | 11 -t "$targetsFilePath" |
| 12 #if str($sideCompoundFile) != 'None': | 12 #if str($sideCompoundFile) != 'None': |
| 13 -sc "$sideCompoundFile" | 13 -sc "$sideCompoundFile" |
| 36 <outputs> | 36 <outputs> |
| 37 <data format="txt" name="output"/> | 37 <data format="txt" name="output"/> |
| 38 </outputs> | 38 </outputs> |
| 39 <tests> | 39 <tests> |
| 40 <test> | 40 <test> |
| 41 | |
| 41 <param name="sbmlFilePath" value="toy_model.xml"/> | 42 <param name="sbmlFilePath" value="toy_model.xml"/> |
| 43 | |
| 42 <param name="targetsFilePath" value="targets.txt"/> | 44 <param name="targetsFilePath" value="targets.txt"/> |
| 45 | |
| 43 <param name="format" value="gml"/> | 46 <param name="format" value="gml"/> |
| 47 | |
| 44 <output ftype="txt" name="output"> | 48 <output ftype="txt" name="output"> |
| 49 | |
| 45 <assert_contents> | 50 <assert_contents> |
| 51 | |
| 46 <has_line_matching expression=".*node.*" n="13"/> | 52 <has_line_matching expression=".*node.*" n="13"/> |
| 53 | |
| 47 <has_line_matching expression=".*edge.*" n="15"/> | 54 <has_line_matching expression=".*edge.*" n="15"/> |
| 55 | |
| 48 </assert_contents> | 56 </assert_contents> |
| 57 | |
| 49 </output> | 58 </output> |
| 59 | |
| 50 </test> | 60 </test> |
| 51 </tests> | 61 </tests> |
| 52 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. | 62 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
| 53 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help> | 63 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help> |
| 54 <citations/> | 64 <citations/> |