Mercurial > repos > metexplore > met4j

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
2 <tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.1">
4
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
3 <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
4 <xrefs>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
6 </xrefs>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
7 <requirements>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
4
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
9 </requirements>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type):
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
11 -f "$type"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
12 #end if
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
13 #if str($smileFile):
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
14 -sm "$smileFile"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
15 #end if
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
16 #if str($inchiFile):
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
17 -in "$inchiFile"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
18 #end if
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
19 $dist
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
20 -s "$inputPath"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
21 #if str($inputSide) != 'None':
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
22 -sc "$inputSide"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
23 #end if
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
24 #if str($mergingStrat):
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
25 -mc "$mergingStrat"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
26 #end if
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
27 $mergeEdges
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
28 $undirected
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
29 $computeWeight
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
30 $removeNaN
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
31 -o "$outputPath"
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
32 ]]></command>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
33 <inputs>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
34 <param argument="-f" label="The chemical fingerprint to use" name="type" optional="true" type="select" value="Extended">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
35 <option value="EState">EState</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
36 <option selected="true" value="Extended">Extended</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
37 <option value="KlekotaRoth">KlekotaRoth</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
38 <option value="MACCS">MACCS</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
39 <option value="PubChem">PubChem</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
40 </param>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
41 <param argument="-sm" label="If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as SMILE string, no header. Ignored if inchi file is provided" name="smileFile" optional="true" type="text" value="">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
42 <sanitizer invalid_char="_">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
43 <valid initial="string.printable"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
44 </sanitizer>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
45 </param>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
46 <param argument="-in" label="If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as InChI string, no header." name="inchiFile" optional="true" type="text" value="">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
47 <sanitizer invalid_char="_">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
48 <valid initial="string.printable"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
49 </sanitizer>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
50 </param>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
51 <param argument="-d" checked="false" falsevalue="" label="Use distance rather than similarity" name="dist" truevalue="-d" type="boolean" value="false"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
52 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
53 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
4
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
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">
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
55 <option selected="true" value="no">no</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
56 <option value="by_name">by_name</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
57 <option value="by_id">by_id</option>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
58 </param>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
59 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
60 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
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"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
62 <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
63 </inputs>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
64 <outputs>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
65 <data format="tsv" name="outputPath"/>
4
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
66 </outputs>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
67 <tests/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
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>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
69 <citations/>
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
metexplore
parents:
diff changeset
70 </tool>