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comparison tools/networkAnalysis/MetaboRank/MetaboRank.xml @ 7:1436e9cde9c9 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
parents 7a6f2380fc1d
children 1274e2a62479
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6:7a6f2380fc1d 7:1436e9cde9c9
40 <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/> 40 <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
41 </inputs> 41 </inputs>
42 <outputs> 42 <outputs>
43 <data format="tsv" name="output"/> 43 <data format="tsv" name="output"/>
44 </outputs> 44 </outputs>
45 <tests/> 45 <tests>
46 <test>
47 <param name="sbmlFilePath" value="XF_network.sbml"/>
48 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
49 <param name="inputSide" value="XF_network_C_Side.tab"/>
50 <output name="output">
51 <assert_contents>
52 <has_n_lines n="1100"/>
53 <has_n_columns n="11"/>
54 </assert_contents>
55 </output>
56 </test>
57 </tests>
46 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. 58 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
47 The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network. 59 The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.
48 The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining. 60 The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
49 It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks. 61 It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
50 See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help> 62 See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help>