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comparison build/tools/MetaboRank/MetaboRank.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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10:6a112eaf8f38 11:40c15b7467f1
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="2.0.0"> 2 <tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.1">
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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</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>
47
47 <param name="sbmlFilePath" value="XF_network.sbml"/> 48 <param name="sbmlFilePath" value="XF_network.sbml"/>
49
48 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/> 50 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
51
49 <param name="inputSide" value="XF_network_C_Side.tab"/> 52 <param name="inputSide" value="XF_network_C_Side.tab"/>
53
50 <output name="output"> 54 <output name="output">
55
51 <assert_contents> 56 <assert_contents>
57
52 <has_n_lines n="1100"/> 58 <has_n_lines n="1100"/>
59
53 <has_n_columns n="11"/> 60 <has_n_columns n="11"/>
61
54 </assert_contents> 62 </assert_contents>
63
55 </output> 64 </output>
65
56 </test> 66 </test>
57 </tests> 67 </tests>
58 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network. 68 <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. 69 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. 70 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.