Mercurial > repos > recetox > matchms

comparison matchms_similarity.xml @ 12:eedbc8f7267f 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 16:02:16 +0000
parents ba9410f612bc
children cfa8b66fb106
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11:ba9410f612bc 12:eedbc8f7267f
1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8"> 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> 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>
23 <configfiles> 23 <configfiles>
24 <configfile name="matchms_python_cli"> 24 <configfile name="matchms_python_cli">
25 python3 ${__tool_directory__}/matchms_similarity_wrapper.py \ 25 python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
26 #if $ri_filtering.is_true 26 #if $ri_filtering.is_true
27 -r $ri_filtering.tolerance \ 27 -r $ri_filtering.tolerance \
28 #end if 28 #end if
29 #if $symmetric.is_symmetric 29 #if $symmetric.is_symmetric
30 -s \ 30 -s \
31 #else 31 #else
32 --ref "$references" \ 32 --ref "$references" \
33 --ref_format "$references.ext" \ 33 --ref_format "$references.ext" \
132 <param name="queries" value="similarity/fill2.msp" ftype="msp"/> 132 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
133 <param name="ri_filtering.is_true" value="TRUE" /> 133 <param name="ri_filtering.is_true" value="TRUE" />
134 <param name="ri_filtering.tolerance" value="60.0" /> 134 <param name="ri_filtering.tolerance" value="60.0" />
135 <param name="similarity_metric" value="CosineGreedy"/> 135 <param name="similarity_metric" value="CosineGreedy"/>
136 <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/> 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"/> 137 <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
138 </test> 138 </test>
139 </tests> 139 </tests>
140 140
141 <help> 141 <help>
142 <![CDATA[ 142 <![CDATA[