Mercurial > repos > metexplore > met4j
comparison build/tools/MetaboRank/MetaboRank.xml @ 7:1436e9cde9c9 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author | metexplore |
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date | Tue, 04 Jul 2023 10:21:26 +0000 |
parents | 7a6f2380fc1d |
children | 1274e2a62479 |
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6:7a6f2380fc1d | 7:1436e9cde9c9 |
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1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
2 <tool id="met4j_MetaboRank" name="MetaboRank" version="1.3.0"> | 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="1.4.0"> |
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:1.3.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</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" |
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> |