Mercurial > repos > metexplore > met4j_extractsubbipnetwork

comparison ExtractSubBipNetwork.xml @ 3:dc9011ea45f6 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 15:29:07 +0000
parents 56501f9a2a6b
children
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2:e362dda04176 3:dc9011ea45f6
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="toy_model.xml"/>
57 <param name="sourcePath" value="seeds.txt"/>
58 <param name="targetPath" value="targets.txt"/>
59 <param name="sideCompoundFile" value="sc.txt"/>
60 <param name="format" value="gml"/>
61 <output ftype="txt" name="output">
62 <assert_contents>
63 <has_line_matching expression=".*node.*" n="5"/>
64 <has_line_matching expression=".*edge.*" n="4"/>
65 </assert_contents>
66 </output>
67 </test>
68 </tests>
69 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. 56 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
70 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. 57 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list.
71 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used. 58 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.
72 @ATTRIBUTION@]]></help> 59 @ATTRIBUTION@]]></help>
73 <citations/> 60 <citations/>