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comparison build/tools/ScopeNetwork/ScopeNetwork.xml @ 11:40c15b7467f1 draft default tip

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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
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>