Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/CompoundNet/CompoundNet.xml @ 1:9b162ee6ff8e draft
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 |
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| 0:dcd16521b969 | 1:9b162ee6ff8e |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="met4j_CompoundNet" name="CompoundNet" version="0.11.0"> | 2 <tool id="met4j_CompoundNet" name="CompoundNet" version="0.12.0"> |
| 3 <description>Advanced creation of a compound graph representation of a SBML file content</description> | 3 <description>Advanced creation of a compound graph representation of a SBML file content</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.CompoundNet -s "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath" |
| 11 #if str($inputSide) != 'None': | 11 #if str($inputSide) != 'None': |
| 12 -sc "$inputSide" | 12 -sc "$inputSide" |
| 13 #end if | 13 #end if |
| 72 </test> | 72 </test> |
| 73 </tests> | 73 </tests> |
| 74 <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. | 74 <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. |
| 75 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. | 75 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. |
| 76 In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> | 76 In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> |
| 77 <citations/> | |
| 77 </tool> | 78 </tool> |