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comparison tools/networkAnalysis/MetaboRank/MetaboRank.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_MetaboRank" name="MetaboRank" version="0.11.0">
3 <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
11 -s "$seedsFilePath"
12 #if str($edgeWeightsFilePaths) != 'None':
13 -w "$edgeWeightsFilePaths"
14 #end if
15 #if str($maxNbOfIter):
16 -max "$maxNbOfIter"
17 #end if
18 #if str($tolerance) != 'nan':
19 -t "$tolerance"
20 #end if
21 #if str($dampingFactor) != 'nan':
22 -d "$dampingFactor"
23 #end if
24 -o "$output"
25 ]]></command>
26 <inputs>
27 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing centrality, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
28 <param argument="-s" format="tsv" label="input seeds file: tabulated file containing node of interest ids and weight" name="seedsFilePath" optional="false" type="data" value=""/>
29 <param argument="-w" format="tsv" label="input edge weight file: (recommended) path to file containing edges' weights. Will be normalized as transition probabilities" name="edgeWeightsFilePaths" optional="true" type="data" value=""/>
30 <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000">
31 <sanitizer invalid_char="_">
32 <valid initial="string.printable"/>
33 </sanitizer>
34 </param>
35 <param argument="-t" label="convergence tolerance" name="tolerance" optional="true" type="float" value="0.001"/>
36 <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
37 </inputs>
38 <outputs>
39 <data format="tsv" name="output"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="inputPath" value="toy_model.xml"/>
44 <output ftype="tsv" name="output">
45 </output>
46 </test>
47 </tests>
48 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
49 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.
50 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.
51 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.
52 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>
53 </tool>