annotate matchms_metadata_match.xml @ 1:b5b360897004 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:26:40 +0000
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1 <tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>matchms metadata match calculation for numeric fields based on tolerance</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>help.xml</import>
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7 </macros>
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8 <expand macro="creator"/>
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9 <expand macro="bio.tools"/>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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13 </requirements>
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15 <command detect_errors="exit_code"><![CDATA[
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16 python3 '${python_wrapper}'
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17 ]]> </command>
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18
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19 <environment_variables>
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20 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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21 </environment_variables>
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23 <configfiles>
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24 <configfile name="python_wrapper">
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25 @init_logger@
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27 from matchms.similarity import MetadataMatch
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29 #if $matching.matching_type == "difference"
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30 tolerance=$matching.tolerance
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31 name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}_${matching.tolerance}"
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32 #else
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33 tolerance=0
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34 name="MetadataMatch_${matching.metadata_match_field}_${matching.matching_type}"
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35 #end if
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37 similarity = MetadataMatch(field="${matching.metadata_match_field}", matching_type="${matching.matching_type}", tolerance=tolerance)
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39 @init_scores@
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41 layer = similarity.matrix(
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42 references=scores.references,
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43 queries=scores.queries,
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44 array_type = "sparse",
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45 is_symmetric=False)
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47 #if $matching.matching_type == "equal_match"
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48 scores._scores.add_dense_matrix(layer, name, join_type=join_type)
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49 #else
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50 scores._scores.add_sparse_data(layer.row, layer.col, layer.data, name, join_type=join_type)
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51 #end if
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52 scores.to_json("$scores_out")
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53 </configfile>
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54 </configfiles>
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55
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56 <inputs>
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57 <expand macro="input_param"/>
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58 <conditional name="matching">
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59 <param label="Matching type" name="matching_type" type="select" display="radio"
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60 help="Type of matching to perform.">
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61 <option value="difference" selected="true">difference</option>
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62 <option value="equal_match">equal match</option>
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63 </param>
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64 <when value="difference">
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65 <param label="Metadata Match" name="metadata_match_field" type="select" display="radio"
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66 help="Metadata field to use for matching.">
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67 <option value="retention_index" selected="true">Retention Index</option>
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68 <option value="retention_time">Retention Time</option>
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69 <option value="precursor_mz">Precursor Mz</option>
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70 </param>
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71 <param label="Tolerance" name="tolerance" type="float" value="0"
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72 help="Tolerance for matching the selected metadata field - only pairs within the tolerance will be contained in the output." />
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73 </when>
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74 <when value="equal_match">
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75 <param label="Metadata Match" name="metadata_match_field" type="select" display="radio"
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76 help="Metadata field to use for matching">
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77 <option value="smiles" selected="true">SMILES</option>
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78 <option value="inchi">InChI</option>
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79 <option value="inchikey">InChIKey</option>
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80 </param>
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81 </when>
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82 </conditional>
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83 </inputs>
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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>