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comparison ExtractSubNetwork.xml @ 3:042795768940 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 15:29:14 +0000
parents 27be7e97f255
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2:27be7e97f255 3:042795768940
46 <option value="gml">gml</option> 46 <option value="gml">gml</option>
47 <option selected="true" value="tab">tab</option> 47 <option selected="true" value="tab">tab</option>
48 <option value="nodeList">nodeList</option> 48 <option value="nodeList">nodeList</option>
49 <option value="json">json</option> 49 <option value="json">json</option>
50 <option value="matrix">matrix</option> 50 <option value="matrix">matrix</option>
51 <option value="jsonviz">jsonviz</option>
51 </param> 52 </param>
52 </inputs> 53 </inputs>
53 <outputs> 54 <outputs>
54 <data format="txt" name="output"/> 55 <data format="txt" name="output"/>
55 </outputs> 56 </outputs>
56 <tests> 57 <tests/>
57 <test>
58 <param name="inputPath" value="toy_model.xml"/>
59 <param name="sourcePath" value="seeds.txt"/>
60 <param name="targetPath" value="targets.txt"/>
61 <param name="format" value="gml"/>
62 <output ftype="txt" name="output">
63 <assert_contents>
64 <has_line_matching expression=".*node.*" n="3"/>
65 <has_line_matching expression=".*edge.*" n="2"/>
66 </assert_contents>
67 </output>
68 </test>
69 </tests>
70 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. 58 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.
71 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list. 59 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list.
72 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. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting. 60 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. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting.
73 See previous works on subnetwork extraction for parameters recommendations. 61 See previous works on subnetwork extraction for parameters recommendations.
74 @ATTRIBUTION@]]></help> 62 @ATTRIBUTION@]]></help>
75 <citations> 63 <citations>
64 <citation type="doi">10.1093/nar/gki437</citation>
65 <citation type="doi">10.1093/bioinformatics/btu760</citation>
66 <citation type="doi">10.1093/bib/bbv115</citation>
67 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
68 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
69 <citation type="doi">10.1093/nar/gki437</citation>
70 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
71 <citation type="doi">10.1093/bioinformatics/btg217</citation>
76 <citation type="doi">10.1093/bib/bbv115</citation> 72 <citation type="doi">10.1093/bib/bbv115</citation>
77 <citation type="doi">10.1093/bioinformatics/bti116</citation> 73 <citation type="doi">10.1093/bioinformatics/bti116</citation>
78 <citation type="doi">10.1093/nar/gki437</citation>
79 <citation type="doi">10.1093/bioinformatics/btg217</citation>
80 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
81 <citation type="doi">10.1093/bioinformatics/btu760</citation> 74 <citation type="doi">10.1093/bioinformatics/btu760</citation>
82 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
83 </citations> 75 </citations>
84 </tool> 76 </tool>