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comparison tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml @ 5:35c9abcd8934 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
comparison
equal deleted inserted replaced
4:ae4c301919c4 5:35c9abcd8934
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.0"> 2 <tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.1">
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:1.2.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</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):
48 <valid initial="string.printable"/> 48 <valid initial="string.printable"/>
49 </sanitizer> 49 </sanitizer>
50 </param> 50 </param>
51 <param argument="-d" checked="false" falsevalue="" label="Use distance rather than similarity" name="dist" truevalue="-d" type="boolean" value="false"/> 51 <param argument="-d" checked="false" falsevalue="" label="Use distance rather than similarity" name="dist" truevalue="-d" type="boolean" value="false"/>
52 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 52 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
53 <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> 53 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
54 <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no"> 54 <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
55 <option selected="true" value="no">no</option> 55 <option selected="true" value="no">no</option>
56 <option value="by_name">by_name</option> 56 <option value="by_name">by_name</option>
57 <option value="by_id">by_id</option> 57 <option value="by_id">by_id</option>
58 </param> 58 </param>
60 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> 60 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
61 <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> 61 <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
62 <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/> 62 <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data format="" 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. 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>
69 <citations/> 69 <citations/>
70 </tool> 70 </tool>