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comparison build/tools/MetaboRank/MetaboRank.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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9:0976a6257300 10:6a112eaf8f38
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_MetaboRank" name="MetaboRank" version="develop"> 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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"
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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58 <param name="sbmlFilePath" value="XF_network.sbml"/> 47 <param name="sbmlFilePath" value="XF_network.sbml"/>
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70 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> 48 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
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82 <param name="inputSide" value="XF_network_C_Side.tab"/> 49 <param name="inputSide" value="XF_network_C_Side.tab"/>
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94 <output name="output"> 50 <output name="output">
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106 <assert_contents> 51 <assert_contents>
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118 <has_n_lines n="1100"/> 52 <has_n_lines n="1100"/>
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130 <has_n_columns n="11"/> 53 <has_n_columns n="11"/>
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142 </assert_contents> 54 </assert_contents>
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154 </output> 55 </output>
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166 </test> 56 </test>
167 </tests> 57 </tests>
168 <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.
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. 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.
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. 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.