Mercurial > repos > metexplore > met4j
comparison build/tools/ScopeNetwork/ScopeNetwork.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_ScopeNetwork" name="ScopeNetwork" version="2.0.0"> | 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.1"> |
| 3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description> | 3 <description>Perform a network expansion from a set of compound seeds to create a scope 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.ScopeNetwork -i "$sbmlFilePath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" |
| 11 -s "$seedsFilePath" | 11 -s "$seedsFilePath" |
| 12 #if str($sideCompoundFile) != 'None': | 12 #if str($sideCompoundFile) != 'None': |
| 13 -sc "$sideCompoundFile" | 13 -sc "$sideCompoundFile" |
| 40 <outputs> | 40 <outputs> |
| 41 <data format="txt" name="output"/> | 41 <data format="txt" name="output"/> |
| 42 </outputs> | 42 </outputs> |
| 43 <tests> | 43 <tests> |
| 44 <test> | 44 <test> |
| 45 | |
| 45 <param name="sbmlFilePath" value="toy_model.xml"/> | 46 <param name="sbmlFilePath" value="toy_model.xml"/> |
| 47 | |
| 46 <param name="seedsFilePath" value="seeds.txt"/> | 48 <param name="seedsFilePath" value="seeds.txt"/> |
| 49 | |
| 47 <param name="sideCompoundFile" value="sides.txt"/> | 50 <param name="sideCompoundFile" value="sides.txt"/> |
| 51 | |
| 48 <param name="format" value="gml"/> | 52 <param name="format" value="gml"/> |
| 53 | |
| 49 <output ftype="txt" name="output"> | 54 <output ftype="txt" name="output"> |
| 55 | |
| 50 <assert_contents> | 56 <assert_contents> |
| 57 | |
| 51 <has_line_matching expression=".*node.*" n="9"/> | 58 <has_line_matching expression=".*node.*" n="9"/> |
| 59 | |
| 52 <has_line_matching expression=".*edge.*" n="11"/> | 60 <has_line_matching expression=".*edge.*" n="11"/> |
| 61 | |
| 53 </assert_contents> | 62 </assert_contents> |
| 63 | |
| 54 </output> | 64 </output> |
| 65 | |
| 55 </test> | 66 </test> |
| 56 </tests> | 67 </tests> |
| 57 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network | 68 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network |
| 58 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction]]></help> | 69 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction]]></help> |
| 59 <citations> | 70 <citations> |