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comparison tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml @ 1:9b162ee6ff8e draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
author metexplore
date Mon, 27 Jun 2022 13:41:08 +0000
parents dcd16521b969
children e69a78624877
comparison
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0:dcd16521b969 1:9b162ee6ff8e
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.11.0"> 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.12.0">
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:0.11.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</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"
44 </test> 44 </test>
45 </tests> 45 </tests>
46 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network 46 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
47 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 47 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
48 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help> 48 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help>
49 <citations/>
49 </tool> 50 </tool>