Mercurial > repos > recetox > matchms_remove_spectra
diff macros.xml @ 0:80df426e7e47 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
author | recetox |
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date | Thu, 30 May 2024 18:07:29 +0000 |
parents | |
children | fbe335d27d25 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 30 18:07:29 2024 +0000 @@ -0,0 +1,107 @@ +<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>