Mercurial > repos > recetox > matchms

comparison matchms_similarity.xml @ 0:30e680e555d4 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author recetox
date Tue, 22 Mar 2022 16:07:32 +0000
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children f680068b7863
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-1:000000000000 0:30e680e555d4
1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy1" python_template_version="3.8">
2 <description>calculate the similarity score and matched peaks</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="creator"/>
8
9 <requirements>
10 <requirement type="package" version="1.1.4">pandas</requirement>
11 <requirement type="package" version="0.55.1">numba</requirement>
12 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
13 </requirements>
14
15 <environment_variables>
16 <environment_variable name="MPLCONFIGDIR">/tmp</environment_variable>
17 </environment_variables>
18
19 <command detect_errors="exit_code"><![CDATA[
20 sh ${matchms_python_cli}
21 ]]> </command>
22
23 <configfiles>
24 <configfile name="matchms_python_cli">
25 python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
26 #if $ri_filtering.is_true
27 -r $ri_filtering.tolerance \
28 #end if
29 #if $symmetric.is_symmetric
30 -s \
31 #else
32 --ref "$references" \
33 --ref_format "$references.ext" \
34 #end if
35 "$queries" \
36 "$queries.ext" \
37 "$similarity_metric" \
38 "$algorithm.tolerance" \
39 "$algorithm.mz_power" \
40 "$algorithm.intensity_power" \
41 "$similarity_scores" \
42 "$similarity_matches"
43 </configfile>
44 </configfiles>
45
46 <inputs>
47 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
48 help="Query mass spectra to match against references."/>
49 <conditional name="symmetric">
50 <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE"
51 checked="false"/>
52 <when value="FALSE">
53 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
54 help="Reference mass spectra to match against as library."/>
55 </when>
56 </conditional>
57 <param label="Similarity metric" name="similarity_metric" type="select" display="radio"
58 help="Similarity metric to use for score computation.">
59 <option value="CosineGreedy" selected="true">CosineGreedy</option>
60 <option value="CosineHungarian">CosineHungarian</option>
61 <option value="ModifiedCosine">ModifiedCosine</option>
62 </param>
63
64 <section name="algorithm" title="Algorithm Parameters" expanded="true">
65 <param label="tolerance" name="tolerance" type="float" value="0.1"
66 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
67 <param label="mz_power" name="mz_power" type="float" value="0.0"
68 help="The power to raise mz to in the cosine function."/>
69 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
70 help="The power to raise intensity to in the cosine function."/>
71 </section>
72
73 <conditional name="ri_filtering">
74 <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE"
75 checked="false"/>
76 <when value="TRUE">
77 <param label="tolerance" name="tolerance" type="float" value="60"
78 help="Peaks will be considered a match when less than tolerance apart."/>
79 </when>
80 </conditional>
81 </inputs>
82
83 <outputs>
84 <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="tsv"/>
85 <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="tsv"/>
86 </outputs>
87
88 <tests>
89 <test>
90 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
91 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
92 <param name="similarity_metric" value="CosineGreedy"/>
93 <output name="similarity_scores" file="similarity/scores_test1_out.tsv" ftype="tsv"
94 checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/>
95 <output name="similarity_matches" file="similarity/matches_test1_out.tsv" ftype="tsv"
96 checksum="md5$aab26ef4a0e80a53699832db72c06340"/>
97 </test>
98 <test>
99 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
100 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
101 <param name="similarity_metric" value="CosineGreedy"/>
102 <output name="similarity_scores" file="scores_test2_out.tsv" ftype="tsv"
103 checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/>
104 <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv"
105 checksum="md5$28dc16ce45105234437e53d59e240046"/>
106 </test>
107 <test>
108 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
109 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
110 <param name="similarity_metric" value="CosineHungarian"/>
111 <output name="similarity_scores" file="similarity/scores_test3_out.tsv" ftype="tsv"
112 checksum="md5$1341369778036e0a267ff723f8cfca9c"/>
113 <output name="similarity_matches" file="similarity/matches_test3_out.tsv" ftype="tsv"
114 checksum="md5$28dc16ce45105234437e53d59e240046"/>
115 </test>
116 <test>
117 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
118 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
119 <param name="similarity_metric" value="ModifiedCosine"/>
120 <output name="similarity_scores" file="similarity/scores_test4_out.tsv" ftype="tsv"/>
121 <output name="similarity_matches" file="similarity/matches_test4_out.tsv" ftype="tsv"/>
122 </test>
123 <test>
124 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
125 <param name="similarity_metric" value="CosineHungarian"/>
126 <param name="is_symmetric" value="TRUE"/>
127 <output name="similarity_scores" file="similarity/scores_test5_out.tsv" ftype="tsv"/>
128 <output name="similarity_matches" file="similarity/matches_test5_out.tsv" ftype="tsv"/>
129 </test>
130 <test>
131 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
132 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
133 <param name="ri_filtering.is_true" value="TRUE" />
134 <param name="ri_filtering.tolerance" value="60.0" />
135 <param name="similarity_metric" value="CosineGreedy"/>
136 <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/>
137 <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
138 </test>
139 </tests>
140
141 <help>
142 <![CDATA[
143 @HELP_matchms@
144 ]]>
145 </help>
146
147 <citations>
148 <citation type="doi">10.5281/zenodo.4589154</citation>
149 <citation type="doi">10.21105/joss.02411</citation>
150 </citations>
151 </tool>