Mercurial > repos > metexplore > met4j

annotate tools/mapping/NameMatcher/NameMatcher.xml @ 6:7a6f2380fc1d 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
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents 35c9abcd8934
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents: 5
diff changeset
2 <tool id="met4j_NameMatcher" name="NameMatcher" version="MET4J_VERSION_TEST">
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
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>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
4 <xrefs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
6 </xrefs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
7 <requirements>
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents: 5
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
9 </requirements>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.NameMatcher#if str($n):
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
11 -nMatch "$n"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
12 #end if
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
13 #if str($nSkip):
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
14 -skip "$nSkip"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
15 #end if
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
16 #if str($col):
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
17 -col "$col"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
18 #end if
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
19 -sbml "$sbml"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
20 -compound "$input"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
21 #if str($comment):
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
22 -c "$comment"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
23 #end if
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
24 #if str($sep):
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
25 -sep "$sep"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
26 #end if
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
27 -o "$outputFile"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
28 ]]></command>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
29 <inputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
30 <param argument="-nMatch" label="[1] Number of match to return per name" name="n" optional="true" type="text" value="1">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
31 <sanitizer invalid_char="_">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
32 <valid initial="string.printable"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
33 </sanitizer>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
34 </param>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
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">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
36 <sanitizer invalid_char="_">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
37 <valid initial="string.printable"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
38 </sanitizer>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
39 </param>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
40 <param argument="-col" label="[1] column containing compounds' names" name="col" optional="true" type="text" value="1">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
41 <sanitizer invalid_char="_">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
42 <valid initial="string.printable"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
43 </sanitizer>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
44 </param>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
45 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
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=""/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
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="#">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
48 <sanitizer invalid_char="_">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
49 <valid initial="string.printable"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
50 </sanitizer>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
51 </param>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
52 <param argument="-sep" label="[\t] separator in the compound file to split the colmumns." name="sep" optional="true" type="text" value="&#9;">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
53 <sanitizer invalid_char="_">
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
54 <valid initial="string.printable"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
55 </sanitizer>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
56 </param>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
57 </inputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
58 <outputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
59 <data format="tsv" name="outputFile"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
60 </outputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
61 <tests/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
62 <help><![CDATA[Metabolic models and Metabolomics Data often refer compounds only by using their common names, which vary greatly according to the source, thus impeding interoperability between models, databases and experimental data. This requires a tedious step of manual mapping. Fuzzy matching is a range of methods which can potentially helps fasten this process, by allowing the search for near-similar names. Fuzzy matching is primarily designed for common language search engines and is frequently based on edit distance, i.e. the number of edits to transform a character string into another, effectively managing typo, case and special character variations, and allowing auto-completion. However, edit-distance based search fall short when mapping chemical names: As an example, alpha-D-Glucose et Glucose would require more edits than between Fructose and Glucose.
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
63
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
64 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.]]></help>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
65 <citations/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
66 </tool>