Mercurial > repos > recetox > matchms_formatter

comparison matchms_formatter.xml @ 10:1b09315a3f87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:59 +0000
parents 966b4134ad12
children ae45992f969e
comparison
equal deleted inserted replaced
9:715fe77be601 10:1b09315a3f87
1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.4" python_template_version="3.5"> 1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>reformat output tables of matchms</description> 2 <description>reformat scores object of matchms to long format table</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import>
6 </macros> 7 </macros>
7 <expand macro="creator"/> 8 <expand macro="creator"/>
9 <edam_operations>
10 <edam_operation>operation_0335</edam_operation>
11 </edam_operations>
12 <expand macro="bio.tools"/>
8 13
9 <requirements> 14 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
11 <requirement type="package" version="1.1.4">pandas</requirement> 16 <requirement type="package" version="1.1.4">pandas</requirement>
12 <requirement type="package" version="8.0.1">click</requirement> 17 <requirement type="package" version="8.0.1">click</requirement>
22 ]]></command> 27 ]]></command>
23 28
24 <configfiles> 29 <configfiles>
25 <configfile name="matchms_formatter_cli"> 30 <configfile name="matchms_formatter_cli">
26 python3 ${__tool_directory__}/formatter.py \ 31 python3 ${__tool_directory__}/formatter.py \
27 --sf "$scores" \ 32 --sf '$scores' \
28 --o "$output" \ 33 --o '$output'
29 $method.selection \
30 #if $method.selection == "get-thresholded-data"
31 --st $method.scores_threshold \
32 --mt $method.matches_threshold
33 #else
34 --k $method.k
35 #end if
36 </configfile> 34 </configfile>
37 </configfiles> 35 </configfiles>
38 36
39 <inputs> 37 <inputs>
40 <param label="Scores object" name="scores" type="data" format="json" help="MatchMS Scores json file." /> 38 <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
41
42 <conditional name="method">
43 <param name="selection" type="select" label="Formatting method">
44 <option value="get-thresholded-data" selected="true">Thresholding</option>
45 <option value="get-top-k-data">Top K Matches</option>
46 </param>
47 <when value="get-thresholded-data">
48 <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
49 help="Threshold for matching score."/>
50 <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
51 help="Threshold for number of matches ions."/>
52 </when>
53 <when value="get-top-k-data">
54 <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
55 </when>
56 </conditional>
57
58 </inputs> 39 </inputs>
59 <outputs> 40 <outputs>
60 <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv"/> 41 <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
61 </outputs> 42 </outputs>
62 43
63 <tests> 44 <tests>
64 <test> 45 <test>
65 <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/> 46 <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
66 <param name="selection" value="get-thresholded-data"/> 47 <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
67 <param name="scores_threshold" value="0.4"/> 48 checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
68 <param name="matches_threshold" value="2"/>
69 <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
70 checksum="md5$db18b3f3dd5d8dea4db0fc1d59d3db3b"/>
71 </test> 49 </test>
72 <test> 50 <test>
73 <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/> 51 <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
74 <param name="selection" value="get-top-k-data"/> 52 <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
75 <param name="k" value="3"/>
76 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
77 checksum="md5$ff827ec7413acac3d2394330935ace99"/>
78 </test> 53 </test>
79 </tests> 54 </tests>
80 55
81 <help><![CDATA[ 56 <help>
82 @HELP_formatter@ 57 @HELP_formatter@
83 ]]></help> 58 @HELP_matchms@
59 </help>
84 </tool> 60 </tool>