Mercurial > repos > recetox > matchms_fingerprint_similarity
view macros.xml @ 16:ad9d2d1b2b8d draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4
author | recetox |
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date | Tue, 04 Jun 2024 07:12:20 +0000 |
parents | c2d546691b7a |
children | d7b517f2c5fe |
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<macros> <token name="@TOOL_VERSION@">0.25.0</token> <xml name="creator"> <creator> <yield/> <person givenName="Helge" familyName="Hecht" url="https://github.com/hechth" identifier="0000-0001-6744-996X" /> <person givenName="Maksym" familyName="Skoryk" url="https://github.com/maximskorik" identifier="0000-0003-2056-8018" /> <person givenName="Zargham" familyName="Ahmad" url="https://github.com/zargham-ahmad" identifier="0000-0002-6096-224X" /> <person givenName="Wudmir" familyName="Rojas" url="https://github.com/wverastegui" identifier="0000-0001-7036-9987" /> <organization url="https://www.recetox.muni.cz/" email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" name="RECETOX MUNI" /> </creator> </xml> <xml name="bio.tools"> <xrefs> <xref type="bio.tools">matchms</xref> </xrefs> </xml> <xml name="similarity_metrics"> <option value="CosineGreedy" selected="true">CosineGreedy</option> <option value="CosineHungarian">CosineHungarian</option> <option value="ModifiedCosine">ModifiedCosine</option> <option value="NeutralLossesCosine">NeutralLossesCosine</option> </xml> <xml name="similarity_algorithm_params"> <section name="algorithm" title="Algorithm Parameters" expanded="true"> <param label="tolerance [Da]" name="tolerance" type="float" value="0.1" help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/> <param label="mz_power" name="mz_power" type="float" value="0.0" help="The power to raise mz to in the cosine function."/> <param label="intensity_power" name="intensity_power" type="float" value="1.0" help="The power to raise intensity to in the cosine function."/> </section> </xml> <xml name="input_param"> <conditional name="scores"> <param name="use_scores" label="Use Scores Object" type="select"> <option value="False" selected="true">FALSE</option> <option value="True">TRUE</option> </param> <when value="True"> <param label="Scores object" name="scores_in" type="data" format="json" help="Scores objects calculated previously using one of the matchms similarity tools." /> <param label="join type" name="join_type" type="select" display="radio" help="The join type to use for appending scores - see [1] for details."> <option value="left" selected="true">left</option> <option value="inner">inner</option> <option value="right">right</option> <option value="outer">outer</option> </param> </when> <when value="False"> <param label="Queries spectra" name="queries" type="data" format="msp" help="Query mass spectra to match against references."/> <param label="Reference spectra" name="references" type="data" format="msp" help="Reference mass spectra to match against as library."/> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="doi">10.5281/zenodo.7178586</citation> <citation type="doi">10.21105/joss.02411</citation> </citations> </xml> <token name="@init_scores@"> from matchms.importing import load_from_msp, scores_from_json from matchms import Scores #if $scores.use_scores == "True" scores = scores_from_json("$scores_in") join_type = "$scores.join_type" #else scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False) join_type = "left" #end if </token> <token name="@init_logger@"> from matchms import set_matchms_logger_level set_matchms_logger_level("WARNING") </token> </macros>