Mercurial > repos > recetox > matchms_metadata_match
annotate matchms_metadata_match.xml @ 3:651cf2ca74b2 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
author | recetox |
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date | Sun, 19 Nov 2023 14:40:48 +0000 |
parents | be20e19c57e8 |
children | 91b4b0c9a384 |
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be20e19c57e8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a493624c962d820d962bd81c14aceede5d5be5b4
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1 <tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
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03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 <description>matchms metadata match calculation for numeric fields based on tolerance</description> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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3 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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4 <macros> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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5 <import>macros.xml</import> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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6 <import>help.xml</import> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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7 </macros> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8 <expand macro="creator"/> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 <expand macro="bio.tools"/> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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10 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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11 <requirements> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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12 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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13 </requirements> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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14 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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15 <command detect_errors="exit_code"><![CDATA[ |
b5b360897004
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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16 python3 '${python_wrapper}' |
b5b360897004
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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17 ]]> </command> |
b5b360897004
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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18 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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19 <environment_variables> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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20 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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21 </environment_variables> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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22 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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23 <configfiles> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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24 <configfile name="python_wrapper"> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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25 @init_logger@ |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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26 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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27 from matchms.similarity import MetadataMatch |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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28 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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29 #if $matching.matching_type == "difference" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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30 tolerance=$matching.tolerance |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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31 name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}_${matching.tolerance}" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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32 #else |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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33 tolerance=0 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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34 name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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35 #end if |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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36 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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37 similarity = MetadataMatch(field="${matching.metadata_match_field}", matching_type="${matching.matching_type}", tolerance=tolerance) |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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38 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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39 @init_scores@ |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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40 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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41 layer = similarity.matrix( |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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42 references=scores.references, |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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43 queries=scores.queries, |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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44 array_type = "sparse", |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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45 is_symmetric=False) |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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46 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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47 #if $matching.matching_type == "equal_match" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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48 scores._scores.add_dense_matrix(layer, name, join_type=join_type) |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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49 #else |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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50 scores._scores.add_sparse_data(layer.row, layer.col, layer.data, name, join_type=join_type) |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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51 #end if |
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52 scores.to_json("$scores_out") |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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53 </configfile> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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54 </configfiles> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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55 |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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56 <inputs> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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57 <expand macro="input_param"/> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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58 <conditional name="matching"> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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59 <param label="Matching type" name="matching_type" type="select" display="radio" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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60 help="Type of matching to perform."> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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61 <option value="difference" selected="true">difference</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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62 <option value="equal_match">equal match</option> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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63 </param> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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64 <when value="difference"> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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65 <param label="Metadata Match" name="metadata_match_field" type="select" display="radio" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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66 help="Metadata field to use for matching."> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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67 <option value="retention_index" selected="true">Retention Index</option> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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68 <option value="retention_time">Retention Time</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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69 <option value="precursor_mz">Precursor Mz</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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70 </param> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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71 <param label="Tolerance" name="tolerance" type="float" value="0" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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72 help="Tolerance for matching the selected metadata field - only pairs within the tolerance will be contained in the output." /> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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73 </when> |
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74 <when value="equal_match"> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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75 <param label="Metadata Match" name="metadata_match_field" type="select" display="radio" |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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76 help="Metadata field to use for matching"> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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77 <option value="smiles" selected="true">SMILES</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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78 <option value="inchi">InChI</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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79 <option value="inchikey">InChIKey</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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80 </param> |
03bc9b7f40f6
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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81 </when> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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82 </conditional> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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83 </inputs> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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84 |
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85 <outputs> |
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86 <data label="Match $matching.metadata_match_field results of ${on_string}" name="scores_out" format="json"/> |
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87 </outputs> |
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88 |
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89 <tests> |
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90 <test> |
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91 <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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92 <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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93 <param name="tolerance" value="60.0" /> |
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94 <output name="scores_out" value="metadata_match/ri_match_60.json" ftype="json" /> |
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95 </test> |
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96 <test> |
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97 <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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98 <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/> |
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99 <param name="matching_type" value="equal_match" /> |
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100 <param name="metadata_match_field" value="smiles" /> |
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101 <output name="scores_out" value="metadata_match/smiles.json" ftype="json" /> |
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102 </test> |
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103 <test> |
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104 <param name="use_scores" value="True"/> |
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105 <param name="scores_in" value="metadata_match/smiles.json" ftype="json"/> |
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106 <param name="matching_type" value="equal_match" /> |
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107 <param name="metadata_match_field" value="inchikey" /> |
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108 <param name="join_type" value="inner" /> |
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109 <output name="scores_out" value="metadata_match/inchi_key_inner.json" ftype="json" /> |
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110 </test> |
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111 <test> |
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112 <param name="use_scores" value="True"/> |
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113 <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/> |
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114 <param name="tolerance" value="20.0" /> |
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115 <param name="join_type" value="inner" /> |
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116 <output name="scores_out" value="metadata_match/inner_join_ri_20.json" ftype="json" /> |
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117 </test> |
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118 <test> |
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119 <param name="use_scores" value="True"/> |
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120 <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/> |
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121 <param name="tolerance" value="20.0" /> |
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122 <param name="join_type" value="left" /> |
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123 <output name="scores_out" value="metadata_match/left_join_ri_20.json" ftype="json" /> |
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124 </test> |
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125 </tests> |
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126 |
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127 <help> |
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128 Description |
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129 The metadata matching module allows comparing metadata entries to create a mask to use for further computations. |
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130 Numerical metadata can be matched using a tolerance while an exact match is required for categorical metadata. |
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131 The output will be __TRUE__ if the value is within the tolerance or an exact match and __FALSE__ otherwise. |
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132 |
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133 .. rubric:: **Footnotes** |
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134 .. [1] SQL join types explained on LearnSQL_. |
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135 |
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136 .. _LearnSQL: https://learnsql.com/blog/sql-joins-types-explained/ |
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137 |
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138 @HELP_matchms@ |
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139 </help> |
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140 |
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141 <expand macro="citations"/> |
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142 </tool> |