Mercurial > repos > metexplore > met4j_sbml2compoundgraph

comparison Sbml2CompoundGraph.xml @ 3:e4862cbda53a draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:31:36 +0000
parents c6d7b50aa5b9
children
comparison
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2:c6d7b50aa5b9 3:e4862cbda53a
44 <option value="gml">gml</option> 44 <option value="gml">gml</option>
45 <option selected="true" value="tab">tab</option> 45 <option selected="true" value="tab">tab</option>
46 <option value="nodeList">nodeList</option> 46 <option value="nodeList">nodeList</option>
47 <option value="json">json</option> 47 <option value="json">json</option>
48 <option value="matrix">matrix</option> 48 <option value="matrix">matrix</option>
49 <option value="jsonviz">jsonviz</option>
49 </param> 50 </param>
50 </inputs> 51 </inputs>
51 <outputs> 52 <outputs>
52 <data format="txt" name="output"/> 53 <data format="txt" name="output"/>
53 </outputs> 54 </outputs>
54 <tests> 55 <tests/>
55 <test>
56 <param name="inputPath" value="XF_network.sbml"/>
57 <param name="inputSide" value="XF_network_C_Side.tab"/>
58 <param name="format" value="gml"/>
59 <output name="output">
60 <assert_contents>
61 <has_line_matching expression=".*node.*" n="1101"/>
62 <has_line_matching expression=".*edge.*" n="5581"/>
63 </assert_contents>
64 </output>
65 </test>
66 <test>
67 <param name="inputPath" value="XF_network.sbml"/>
68 <param name="inputSide" value="XF_network_C_Side.tab"/>
69 <param name="undirected" value="true"/>
70 <param name="computeWeight" value="true"/>
71 <param name="removeIsolated" value="true"/>
72 <param name="degree" value="true"/>
73 <param name="mergingStrat" value="by_id"/>
74 <param name="format" value="gml"/>
75 <output name="output">
76 <assert_contents>
77 <has_line_matching expression=".*node.*" n="793"/>
78 <has_line_matching expression=".*edge.*" n="9372"/>
79 </assert_contents>
80 </output>
81 </test>
82 </tests>
83 <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. 56 <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.
84 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. 57 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.
85 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 degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network. 58 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 degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.
86 @ATTRIBUTION@]]></help> 59 @ATTRIBUTION@]]></help>
87 <citations/> 60 <citations/>