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comparison tools/networkAnalysis/MetaboRank/MetaboRank.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_MetaboRank" name="MetaboRank" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="develop">
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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</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"
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> 46 <test>
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47 <param name="sbmlFilePath" value="XF_network.sbml"/> 58 <param name="sbmlFilePath" value="XF_network.sbml"/>
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48 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> 70 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
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49 <param name="inputSide" value="XF_network_C_Side.tab"/> 82 <param name="inputSide" value="XF_network_C_Side.tab"/>
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50 <output name="output"> 94 <output name="output">
51 <assert_contents> 95
52 <has_n_lines n="1100"/> 96
53 <has_n_columns n="11"/> 97
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106 <assert_contents>
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118 <has_n_lines n="1100"/>
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130 <has_n_columns n="11"/>
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54 </assert_contents> 142 </assert_contents>
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55 </output> 154 </output>
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56 </test> 166 </test>
57 </tests> 167 </tests>
58 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. 168 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic 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. 169 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.
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. 170 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.
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. 171 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.
62 For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker. 172 For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.
63 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> 173 See publication for more information.]]></help>
64 <citations/> 174 <citations>
175 <citation type="doi">10.1093/bioinformatics/bty577</citation>
176 </citations>
65 </tool> 177 </tool>