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comparison tools/networkAnalysis/ScopeNetwork/ScopeNetwork.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
comparison
equal deleted inserted replaced
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_ScopeNetwork" name="ScopeNetwork" version="develop"> 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.0">
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: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.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
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48 <param name="sbmlFilePath" value="toy_model.xml"/> 45 <param name="sbmlFilePath" value="toy_model.xml"/>
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52 <param name="seedsFilePath" value="seeds.txt"/> 46 <param name="seedsFilePath" value="seeds.txt"/>
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56 <param name="sideCompoundFile" value="sides.txt"/> 47 <param name="sideCompoundFile" value="sides.txt"/>
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60 <param name="format" value="gml"/> 48 <param name="format" value="gml"/>
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64 <output ftype="txt" name="output"> 49 <output ftype="txt" name="output">
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68 <assert_contents> 50 <assert_contents>
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72 <has_line_matching expression=".*node.*" n="9"/> 51 <has_line_matching expression=".*node.*" n="9"/>
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76 <has_line_matching expression=".*edge.*" n="11"/> 52 <has_line_matching expression=".*edge.*" n="11"/>
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80 </assert_contents> 53 </assert_contents>
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84 </output> 54 </output>
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88 </test> 55 </test>
89 </tests> 56 </tests>
90 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network 57 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
91 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> 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>
92 <citations> 59 <citations>