Mercurial > repos > recetox > matchms_formatter

comparison matchms_formatter.xml @ 4:da32f57b4f88 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 5b13d8883fe18bee3aa992c2e34aa1fa79419442"
author recetox
date Fri, 11 Feb 2022 10:33:48 +0000
parents e2a1dbeba196
children 97c61213a872
comparison
equal deleted inserted replaced
3:e2a1dbeba196 4:da32f57b4f88
1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.1" python_template_version="3.5"> 1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.2" python_template_version="3.5">
2 <description>reformat output tables of matchms</description> 2 <description>reformat output tables of matchms</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
30 #end if 30 #end if
31 </configfile> 31 </configfile>
32 </configfiles> 32 </configfiles>
33 33
34 <inputs> 34 <inputs>
35 <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table."/> 35 <param label="Scores Table" name="scores" type="data" format="csv,tabular,tsv" help="Scores output table." />
36 <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table."/> 36 <param label="Matches Table" name="matches" type="data" format="csv,tabular,tsv" help="Scores output table." />
37
37 38
38 <conditional name="method"> 39 <conditional name="method">
39 <param name="selection" type="select" label="Formatting method"> 40 <param name="selection" type="select" label="Formatting method">
40 <option value="get-thresholded-data" selected="true">Thresholding</option> 41 <option value="get-thresholded-data" selected="true">Thresholding</option>
41 <option value="get-top-k-data">Top K Matches</option> 42 <option value="get-top-k-data">Top K Matches</option>
74 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv" 75 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
75 checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/> 76 checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
76 </test> 77 </test>
77 </tests> 78 </tests>
78 79
79 <help> 80 <help><![CDATA[
80 <![CDATA[ 81 Usage
81 @HELP_formatter@ 82 This tool creates user friendly tables from the data matrices produces by matchms.
82 ]]> 83 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
83 </help> 84
85 Input Table Format
86 The tool expects two data matrices with the format as depicted below.
87 The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
88
89 +----------+------+------+-----+
90 | | C001 | C002 | ... |
91 +==========+======+======+=====+
92 | Perylene | 0.1 | 0.0 | ... |
93 +----------+------+------+-----+
94 | Glycine | 0.5 | 0.34 | ... |
95 +----------+------+------+-----+
96 | ... | ... | ... | ... |
97 +----------+------+------+-----+
98
99 Output Table Format
100 +----------+-----------+---------+--------+
101 | query | reference | matches | scores |
102 +==========+===========+=========+========+
103 | C001 | Glycine | 6 | 0.5 |
104 +----------+-----------+---------+--------+
105 | C002 | Glycine | 3 | 0.34 |
106 +----------+-----------+---------+--------+
107 | ... | ... | ... | ... |
108 +----------+-----------+---------+--------+
109
110 ]]></help>
84 </tool> 111 </tool>