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comparison tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.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_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.11.0"> 2 <tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.12.0">
3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> 3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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.CarbonSkeletonNet -s "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
11 -g "$inputAAM" 11 -g "$inputAAM"
12 $keepSingleCarbon 12 $keepSingleCarbon
13 $mergeComp 13 $mergeComp
114 </assert_contents> 114 </assert_contents>
115 </output> 115 </output>
116 </test> 116 </test>
117 </tests> 117 </tests>
118 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help> 118 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>
119 <citations/>
119 </tool> 120 </tool>