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comparison build/tools/ChemSimilarityWeighting/ChemSimilarityWeighting.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_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.5.0"> 2 <tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="develop">
3 <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description> 3 <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</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:1.5.0</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.ChemSimilarityWeighting#if str($type): 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type):
11 -f "$type" 11 -f "$type"
12 #end if 12 #end if
13 #if str($smileFile): 13 #if str($smileFile):
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data format="tsv" name="outputPath"/> 65 <data format="tsv" name="outputPath"/>
66 </outputs> 66 </outputs>
67 <tests/> 67 <tests/>
68 <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217), Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)]]></help> 68 <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help>
69 <citations/> 69 <citations>
70 <citation type="doi">10.1093/bioinformatics/btg217</citation>
71 <citation type="doi">10.1093/bioinformatics/bti116</citation>
72 <citation type="doi">10.1093/bioinformatics/btu760</citation>
73 </citations>
70 </tool> 74 </tool>