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comparison build/tools/PrecursorNetwork/PrecursorNetwork.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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9:0976a6257300 10:6a112eaf8f38
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="develop"> 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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>
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44 <param name="sbmlFilePath" value="toy_model.xml"/> 41 <param name="sbmlFilePath" value="toy_model.xml"/>
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48 <param name="targetsFilePath" value="targets.txt"/> 42 <param name="targetsFilePath" value="targets.txt"/>
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52 <param name="format" value="gml"/> 43 <param name="format" value="gml"/>
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56 <output ftype="txt" name="output"> 44 <output ftype="txt" name="output">
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60 <assert_contents> 45 <assert_contents>
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64 <has_line_matching expression=".*node.*" n="13"/> 46 <has_line_matching expression=".*node.*" n="13"/>
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68 <has_line_matching expression=".*edge.*" n="15"/> 47 <has_line_matching expression=".*edge.*" n="15"/>
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72 </assert_contents> 48 </assert_contents>
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76 </output> 49 </output>
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80 </test> 50 </test>
81 </tests> 51 </tests>
82 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. 52 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network.
83 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> 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>
84 <citations/> 54 <citations/>