Mercurial > repos > recetox > matchms

annotate matchms_similarity.xml @ 6:ff2455f76a26 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
author recetox
date Thu, 27 Apr 2023 12:01:41 +0000
parents 28f7f2e60331
children
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ba5e9bd05d5b planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8">
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2 <description>calculate the similarity score and matched peaks</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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9 <requirements>
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10 <requirement type="package" version="1.1.4">pandas</requirement>
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11 <requirement type="package" version="0.55.1">numba</requirement>
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12 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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13 </requirements>
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15 <environment_variables>
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16 <environment_variable name="MPLCONFIGDIR">/tmp</environment_variable>
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17 </environment_variables>
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19 <command detect_errors="exit_code"><![CDATA[
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20 sh ${matchms_python_cli}
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21 ]]> </command>
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23 <configfiles>
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24 <configfile name="matchms_python_cli">
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25 python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
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26 #if $ri_filtering.is_true
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27 -r $ri_filtering.tolerance \
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28 #end if
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29 #if $symmetric.is_symmetric
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30 -s \
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31 #else
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32 --ref "$references" \
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33 --ref_format "$references.ext" \
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34 #end if
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35 "$queries" \
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36 "$queries.ext" \
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37 "$similarity_metric" \
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38 "$algorithm.tolerance" \
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39 "$algorithm.mz_power" \
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40 "$algorithm.intensity_power" \
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41 "$similarity_scores" \
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42 </configfile>
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43 </configfiles>
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44
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45 <inputs>
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46 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
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47 help="Query mass spectra to match against references."/>
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48 <conditional name="symmetric">
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49 <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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50 checked="false"/>
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51 <when value="FALSE">
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52 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
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53 help="Reference mass spectra to match against as library."/>
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54 </when>
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55 </conditional>
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56 <param label="Similarity metric" name="similarity_metric" type="select" display="radio"
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57 help="Similarity metric to use for score computation.">
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58 <option value="CosineGreedy" selected="true">CosineGreedy</option>
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59 <option value="CosineHungarian">CosineHungarian</option>
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60 <option value="ModifiedCosine">ModifiedCosine</option>
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61 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
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62 </param>
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64 <section name="algorithm" title="Algorithm Parameters" expanded="true">
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65 <param label="tolerance" name="tolerance" type="float" value="0.1"
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66 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
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67 <param label="mz_power" name="mz_power" type="float" value="0.0"
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68 help="The power to raise mz to in the cosine function."/>
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69 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
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70 help="The power to raise intensity to in the cosine function."/>
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71 </section>
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73 <conditional name="ri_filtering">
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74 <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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75 checked="false"/>
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76 <when value="TRUE">
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77 <param label="tolerance" name="tolerance" type="float" value="60"
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78 help="Peaks will be considered a match when less than tolerance apart."/>
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79 </when>
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80 </conditional>
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81 </inputs>
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82
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83 <outputs>
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84 <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="json"/>
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85 </outputs>
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86
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87 <tests>
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88 <test> <!-- TEST #1: Test scoring of different file formats. -->
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89 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
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90 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
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91 <param name="similarity_metric" value="CosineGreedy"/>
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92 <output name="similarity_scores" file="similarity/scores_test1_out.json" ftype="json"
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93 checksum="md5$72f96c48f8c34cf2a7c37d3aede33ca0"/>
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94 </test>
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95 <test> <!-- TEST #2: Test scoring of the same file formats. -->
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96 <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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97 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
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98 <param name="similarity_metric" value="CosineGreedy"/>
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99 <output name="similarity_scores" file="similarity/scores_test2_out.json" ftype="json"
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100 checksum="md5$d325a895f74262087553d08cc40a99aa"/>
0
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101 </test>
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102 <test> <!-- TEST #3: Test scoring with applying RI filtering. -->
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103 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
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104 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
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105 <conditional name="ri_filtering">
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106 <param name="is_true" value="True"></param>
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107 <param name="tolerance" value="60.0" />
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108 </conditional>
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109 <param name="similarity_metric" value="CosineHungarian"/>
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110 <output name="similarity_scores" file="similarity/scores_test3_out.json" ftype="json"
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111 checksum="md5$437c03775ebe978f03b7c63aa09ee52e"/>
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112 </test>
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113 <test> <!-- TEST #4: Test symmetric scoring. -->
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114 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
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115 <param name="is_symmetric" value="TRUE"/>
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116 <param name="similarity_metric" value="NeutralLossesCosine"/>
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117 <output name="similarity_scores" file="similarity/scores_test4_out.json" ftype="json"
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118 checksum="md5$951b3bad2207d8301e0c60397533e607"/>
1
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119 </test>
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120 <test> <!-- TEST #5: Test symmetric scoring with applying RI filtering. -->
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121 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
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122 <param name="similarity_metric" value="ModifiedCosine"/>
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123 <param name="is_symmetric" value="TRUE" />
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124 <conditional name="ri_filtering">
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125 <param name="is_true" value="True"></param>
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126 <param name="tolerance" value="60.0" />
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127 </conditional>
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128 <output name="similarity_scores" file="similarity/scores_test5_out.json" ftype="json"
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129 checksum="md5$31f83451443a1996fbd7fbc204803481"/>
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130 </test>
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131 </tests>
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132
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133 <help>
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134 <![CDATA[
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135 @HELP_matchms@
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136 ]]>
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137 </help>
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138
5
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139 <expand macro="citations"/>
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140 </tool>