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comparison tools/networkAnalysis/MetaboRank/MetaboRank.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents 35c9abcd8934
children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_MetaboRank" name="MetaboRank" version="1.2.1"> 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="MET4J_VERSION_TEST">
3 <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description> 3 <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
11 -s "$seedsFilePath" 11 -s "$seedsFilePath"
12 #if str($edgeWeightsFilePaths) != 'None': 12 #if str($edgeWeightsFilePaths) != 'None':
13 -w "$edgeWeightsFilePaths" 13 -w "$edgeWeightsFilePaths"
14 #end if
15 #if str($inputSide) != 'None':
16 -sc "$inputSide"
14 #end if 17 #end if
15 #if str($maxNbOfIter): 18 #if str($maxNbOfIter):
16 -max "$maxNbOfIter" 19 -max "$maxNbOfIter"
17 #end if 20 #end if
18 #if str($tolerance) != 'nan': 21 #if str($tolerance) != 'nan':
25 ]]></command> 28 ]]></command>
26 <inputs> 29 <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=""/> 30 <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=""/> 31 <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=""/> 32 <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=""/>
33 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
30 <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000"> 34 <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000">
31 <sanitizer invalid_char="_"> 35 <sanitizer invalid_char="_">
32 <valid initial="string.printable"/> 36 <valid initial="string.printable"/>
33 </sanitizer> 37 </sanitizer>
34 </param> 38 </param>
36 <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"/>
37 </inputs> 41 </inputs>
38 <outputs> 42 <outputs>
39 <data format="tsv" name="output"/> 43 <data format="tsv" name="output"/>
40 </outputs> 44 </outputs>
41 <tests> 45 <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. 46 <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. 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.
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. 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.
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. 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.
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> 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>