Mercurial > repos > recetox > matchms_metadata_match
view matchms_metadata_match.xml @ 15:86e080d81cfb 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 18:11:00 +0000 |
parents | 43d40415654c |
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<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>matchms metadata match calculation for numeric fields based on tolerance</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <expand macro="creator"/> <expand macro="bio.tools"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python3 '${python_wrapper}' ]]> </command> <environment_variables> <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> </environment_variables> <configfiles> <configfile name="python_wrapper"> @init_logger@ from matchms.similarity import MetadataMatch #if $matching.matching_type == "difference" tolerance=$matching.tolerance name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}_${matching.tolerance}" #else tolerance=0 name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}" #end if similarity = MetadataMatch(field="${matching.metadata_match_field}", matching_type="${matching.matching_type}", tolerance=tolerance) @init_scores@ layer = similarity.matrix( references=scores.references, queries=scores.queries, array_type = "sparse", is_symmetric=False) scores._scores.add_sparse_data(layer.row, layer.col, layer.data, name, join_type=join_type) scores.to_json("$scores_out") </configfile> </configfiles> <inputs> <expand macro="input_param"/> <conditional name="matching"> <param label="Matching type" name="matching_type" type="select" display="radio" help="Type of matching to perform."> <option value="difference" selected="true">difference</option> <option value="equal_match">equal match</option> </param> <when value="difference"> <param label="Metadata Match" name="metadata_match_field" type="select" display="radio" help="Metadata field to use for matching."> <option value="retention_index" selected="true">Retention Index</option> <option value="retention_time">Retention Time</option> <option value="precursor_mz">Precursor Mz</option> </param> <param label="Tolerance" name="tolerance" type="float" value="0" help="Tolerance for matching the selected metadata field - only pairs within the tolerance will be contained in the output." /> </when> <when value="equal_match"> <param label="Metadata Match" name="metadata_match_field" type="select" display="radio" help="Metadata field to use for matching"> <option value="smiles" selected="true">SMILES</option> <option value="inchi">InChI</option> <option value="inchikey">InChIKey</option> <option value="formula">Formula</option> </param> </when> </conditional> </inputs> <outputs> <data label="Match $matching.metadata_match_field results of ${on_string}" name="scores_out" format="json"/> </outputs> <tests> <test> <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="tolerance" value="60.0" /> <output name="scores_out" value="metadata_match/ri_match_60.json" ftype="json" /> </test> <test> <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="matching_type" value="equal_match" /> <param name="metadata_match_field" value="smiles" /> <output name="scores_out" value="metadata_match/smiles.json" ftype="json" /> </test> <test> <param name="use_scores" value="True"/> <param name="scores_in" value="metadata_match/smiles.json" ftype="json"/> <param name="matching_type" value="equal_match" /> <param name="metadata_match_field" value="inchikey" /> <param name="join_type" value="inner" /> <output name="scores_out" value="metadata_match/inchi_key_inner.json" ftype="json" /> </test> <test> <param name="use_scores" value="True"/> <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/> <param name="tolerance" value="20.0" /> <param name="join_type" value="inner" /> <output name="scores_out" value="metadata_match/inner_join_ri_20.json" ftype="json" /> </test> <test> <param name="use_scores" value="True"/> <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/> <param name="tolerance" value="20.0" /> <param name="join_type" value="left" /> <output name="scores_out" value="metadata_match/left_join_ri_20.json" ftype="json" /> </test> <test> <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> <param name="matching_type" value="equal_match" /> <param name="metadata_match_field" value="formula" /> <output name="scores_out" value="metadata_match/formula.json" ftype="json" /> </test> </tests> <help> Description The metadata matching module allows comparing metadata entries to create a mask to use for further computations. Numerical metadata can be matched using a tolerance while an exact match is required for categorical metadata. The output will be __TRUE__ if the value is within the tolerance or an exact match and __FALSE__ otherwise. .. rubric:: **Footnotes** .. [1] SQL join types explained on W3School_. .. _W3School: https://www.w3schools.com/sql/sql_join.asp @HELP_matchms@ </help> <expand macro="citations"/> </tool>