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comparison tools/mapping/NameMatcher/NameMatcher.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 7a6f2380fc1d
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_NameMatcher" name="NameMatcher" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_NameMatcher" name="NameMatcher" version="develop">
3 <description>This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently.</description> 3 <description>This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently.</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:MET4J_VERSION_TEST</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 mapping.NameMatcher#if str($n): 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n):
11 -nMatch "$n" 11 -nMatch "$n"
12 #end if 12 #end if
13 #if str($nSkip): 13 #if str($nSkip):
14 -skip "$nSkip" 14 -skip "$nSkip"
15 #end if 15 #end if
16 #if str($col): 16 #if str($col):
17 -col "$col" 17 -col "$col"
18 #end if 18 #end if
19 -sbml "$sbml" 19 -i "$sbml"
20 -compound "$input" 20 -compound "$input"
21 #if str($comment): 21 #if str($comment):
22 -c "$comment" 22 -c "$comment"
23 #end if 23 #end if
24 #if str($sep): 24 #if str($sep):
25 -sep "$sep" 25 -sep "$sep"
26 #end if 26 #end if
27 -o "$outputFile" 27 -o "$outputFile"
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param argument="-nMatch" label="[1] Number of match to return per name" name="n" optional="true" type="text" value="1"> 30 <param argument="-nMatch" label="[1] Number of matchs to return per name" name="n" optional="true" type="text" value="1">
31 <sanitizer invalid_char="_"> 31 <sanitizer invalid_char="_">
32 <valid initial="string.printable"/> 32 <valid initial="string.printable"/>
33 </sanitizer> 33 </sanitizer>
34 </param> 34 </param>
35 <param argument="-skip" label="[0] Number of lines to skip at the beginning of the compound file" name="nSkip" optional="true" type="text" value="0"> 35 <param argument="-skip" label="[0] Number of lines to skip at the beginning of the compound file" name="nSkip" optional="true" type="text" value="0">
40 <param argument="-col" label="[1] column containing compounds' names" name="col" optional="true" type="text" value="1"> 40 <param argument="-col" label="[1] column containing compounds' names" name="col" optional="true" type="text" value="1">
41 <sanitizer invalid_char="_"> 41 <sanitizer invalid_char="_">
42 <valid initial="string.printable"/> 42 <valid initial="string.printable"/>
43 </sanitizer> 43 </sanitizer>
44 </param> 44 </param>
45 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> 45 <param argument="-i" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
46 <param argument="-compound" format="tsv" label="Compound file containing one column with compound names to search among the SBML entries" name="input" optional="false" type="data" value=""/> 46 <param argument="-compound" format="tsv" label="Compound file containing one column with compound names to search among the SBML entries" name="input" optional="false" type="data" value=""/>
47 <param argument="-c" label="[#] Comment String in the compound file. The lines beginning by this string won't be read" name="comment" optional="true" type="text" value="#"> 47 <param argument="-c" label="[#] Comment String in the compound file. The lines beginning by this string won't be read" name="comment" optional="true" type="text" value="#">
48 <sanitizer invalid_char="_"> 48 <sanitizer invalid_char="_">
49 <valid initial="string.printable"/> 49 <valid initial="string.printable"/>
50 </sanitizer> 50 </sanitizer>