Mercurial > repos > recetox > matchms

comparison matchms_similarity.xml @ 1:f680068b7863 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
author recetox
date Fri, 22 Jul 2022 16:48:21 +0000
parents 30e680e555d4
children 67ed0d4f3724
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0:30e680e555d4 1:f680068b7863
1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy1" python_template_version="3.8"> 1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8">
2 <description>calculate the similarity score and matched peaks</description> 2 <description>calculate the similarity score and matched peaks</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
57 <param label="Similarity metric" name="similarity_metric" type="select" display="radio" 57 <param label="Similarity metric" name="similarity_metric" type="select" display="radio"
58 help="Similarity metric to use for score computation."> 58 help="Similarity metric to use for score computation.">
59 <option value="CosineGreedy" selected="true">CosineGreedy</option> 59 <option value="CosineGreedy" selected="true">CosineGreedy</option>
60 <option value="CosineHungarian">CosineHungarian</option> 60 <option value="CosineHungarian">CosineHungarian</option>
61 <option value="ModifiedCosine">ModifiedCosine</option> 61 <option value="ModifiedCosine">ModifiedCosine</option>
62 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
62 </param> 63 </param>
63 64
64 <section name="algorithm" title="Algorithm Parameters" expanded="true"> 65 <section name="algorithm" title="Algorithm Parameters" expanded="true">
65 <param label="tolerance" name="tolerance" type="float" value="0.1" 66 <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 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
134 <param name="ri_filtering.tolerance" value="60.0" /> 135 <param name="ri_filtering.tolerance" value="60.0" />
135 <param name="similarity_metric" value="CosineGreedy"/> 136 <param name="similarity_metric" value="CosineGreedy"/>
136 <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/> 137 <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 <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
138 </test> 139 </test>
140 <test>
141 <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
142 <param name="queries" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
143 <param name="similarity_metric" value="NeutralLossesCosine"/>
144 <output name="similarity_scores" file="similarity/scores_test7_out.tsv" ftype="tsv"/>
145 <output name="similarity_matches" file="similarity/matches_test7_out.tsv" ftype="tsv"/>
146 </test>
139 </tests> 147 </tests>
140 148
141 <help> 149 <help>
142 <![CDATA[ 150 <![CDATA[
143 @HELP_matchms@ 151 @HELP_matchms@