Mercurial > repos > metexplore > met4j
comparison build/tools/MetaboRank/MetaboRank.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
| author | metexplore |
|---|---|
| date | Wed, 17 May 2023 13:26:37 +0000 |
| parents | |
| children | 1436e9cde9c9 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="1.3.0"> | |
| 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:1.3.0</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($inputSide) != 'None': | |
| 16 -sc "$inputSide" | |
| 17 #end if | |
| 18 #if str($maxNbOfIter): | |
| 19 -max "$maxNbOfIter" | |
| 20 #end if | |
| 21 #if str($tolerance) != 'nan': | |
| 22 -t "$tolerance" | |
| 23 #end if | |
| 24 #if str($dampingFactor) != 'nan': | |
| 25 -d "$dampingFactor" | |
| 26 #end if | |
| 27 -o "$output" | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 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=""/> | |
| 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=""/> | |
| 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=""/> | |
| 34 <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000"> | |
| 35 <sanitizer invalid_char="_"> | |
| 36 <valid initial="string.printable"/> | |
| 37 </sanitizer> | |
| 38 </param> | |
| 39 <param argument="-t" label="convergence tolerance" name="tolerance" optional="true" type="float" value="0.001"/> | |
| 40 <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <data format="tsv" name="output"/> | |
| 44 </outputs> | |
| 45 <tests/> | |
| 46 <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. | |
| 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. | |
| 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. | |
| 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> | |
| 51 <citations/> | |
| 52 </tool> |