Mercurial > repos > recetox > matchms_metadata_match
diff matchms_metadata_match.xml @ 0:03bc9b7f40f6 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
| author | recetox |
|---|---|
| date | Tue, 27 Jun 2023 14:28:41 +0000 |
| parents | |
| children | b5b360897004 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_metadata_match.xml Tue Jun 27 14:28:41 2023 +0000 @@ -0,0 +1,142 @@ +<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> + + <environment_variables> + <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> + </environment_variables> + + <command detect_errors="exit_code"><![CDATA[ + python3 '${python_wrapper}' + ]]> </command> + +<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) + +#if $matching.matching_type == "equal_match" +scores._scores.add_dense_matrix(layer, name, join_type=join_type) +#else +scores._scores.add_sparse_data(layer.row, layer.col, layer.data, name, join_type=join_type) +#end if +scores.to_json("$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> + </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> + </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 LearnSQL_. + + .. _LearnSQL: https://learnsql.com/blog/sql-joins-types-explained/ + + @HELP_matchms@ + </help> + + <expand macro="citations"/> +</tool>