Mercurial > repos > recetox > matchms

annotate matchms_similarity.xml @ 3:9f8532c99845 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 38a5028a7abe99794086e9b1374ab4bb8bfa68de
author recetox
date Wed, 21 Sep 2022 15:28:55 +0000
parents 67ed0d4f3724
children ba5e9bd05d5b
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9f8532c99845 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 38a5028a7abe99794086e9b1374ab4bb8bfa68de
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1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy2" 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 "$similarity_matches"
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43 </configfile>
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44 </configfiles>
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45
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46 <inputs>
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47 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
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48 help="Query mass spectra to match against references."/>
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49 <conditional name="symmetric">
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50 <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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51 checked="false"/>
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52 <when value="FALSE">
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53 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
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54 help="Reference mass spectra to match against as library."/>
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55 </when>
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56 </conditional>
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57 <param label="Similarity metric" name="similarity_metric" type="select" display="radio"
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58 help="Similarity metric to use for score computation.">
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59 <option value="CosineGreedy" selected="true">CosineGreedy</option>
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60 <option value="CosineHungarian">CosineHungarian</option>
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61 <option value="ModifiedCosine">ModifiedCosine</option>
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62 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
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63 </param>
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64
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65 <section name="algorithm" title="Algorithm Parameters" expanded="true">
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66 <param label="tolerance" name="tolerance" type="float" value="0.1"
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67 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
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68 <param label="mz_power" name="mz_power" type="float" value="0.0"
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69 help="The power to raise mz to in the cosine function."/>
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70 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
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71 help="The power to raise intensity to in the cosine function."/>
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72 </section>
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73
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74 <conditional name="ri_filtering">
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75 <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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76 checked="false"/>
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77 <when value="TRUE">
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78 <param label="tolerance" name="tolerance" type="float" value="60"
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79 help="Peaks will be considered a match when less than tolerance apart."/>
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80 </when>
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81 </conditional>
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82 </inputs>
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83
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84 <outputs>
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85 <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="tsv"/>
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86 <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="tsv"/>
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87 </outputs>
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88
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89 <tests>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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90 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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91 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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92 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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93 <param name="similarity_metric" value="CosineGreedy"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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94 <output name="similarity_scores" file="similarity/scores_test1_out.tsv" ftype="tsv"
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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95 checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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96 <output name="similarity_matches" file="similarity/matches_test1_out.tsv" ftype="tsv"
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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97 checksum="md5$aab26ef4a0e80a53699832db72c06340"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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98 </test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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99 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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100 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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101 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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102 <param name="similarity_metric" value="CosineGreedy"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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103 <output name="similarity_scores" file="scores_test2_out.tsv" ftype="tsv"
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104 checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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105 <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv"
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106 checksum="md5$28dc16ce45105234437e53d59e240046"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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107 </test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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108 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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109 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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110 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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111 <param name="similarity_metric" value="CosineHungarian"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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112 <output name="similarity_scores" file="similarity/scores_test3_out.tsv" ftype="tsv"
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113 checksum="md5$1341369778036e0a267ff723f8cfca9c"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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114 <output name="similarity_matches" file="similarity/matches_test3_out.tsv" ftype="tsv"
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115 checksum="md5$28dc16ce45105234437e53d59e240046"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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116 </test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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117 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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118 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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119 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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120 <param name="similarity_metric" value="ModifiedCosine"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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121 <output name="similarity_scores" file="similarity/scores_test4_out.tsv" ftype="tsv"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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122 <output name="similarity_matches" file="similarity/matches_test4_out.tsv" ftype="tsv"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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123 </test>
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124 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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125 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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126 <param name="similarity_metric" value="CosineHungarian"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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127 <param name="is_symmetric" value="TRUE"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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128 <output name="similarity_scores" file="similarity/scores_test5_out.tsv" ftype="tsv"/>
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129 <output name="similarity_matches" file="similarity/matches_test5_out.tsv" ftype="tsv"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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130 </test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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131 <test>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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132 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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133 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
2
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134 <conditional name="ri_filtering">
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135 <param name="is_true" value="True"></param>
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136 <param name="tolerance" value="60.0" />
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137 </conditional>
0
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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138 <param name="similarity_metric" value="CosineGreedy"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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139 <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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140 <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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141 </test>
1
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142 <test>
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143 <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
f680068b7863 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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144 <param name="queries" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
f680068b7863 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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145 <param name="similarity_metric" value="NeutralLossesCosine"/>
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146 <output name="similarity_scores" file="similarity/scores_test7_out.tsv" ftype="tsv"/>
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147 <output name="similarity_matches" file="similarity/matches_test7_out.tsv" ftype="tsv"/>
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148 </test>
3
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149 <test>
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150 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
9f8532c99845 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 38a5028a7abe99794086e9b1374ab4bb8bfa68de
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151 <param name="similarity_metric" value="CosineGreedy"/>
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152 <param name="is_symmetric" value="TRUE" />
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153 <conditional name="ri_filtering">
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154 <param name="is_true" value="True"></param>
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155 <param name="tolerance" value="60.0" />
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156 </conditional>
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157 <output name="similarity_scores" file="similarity/scores_test8_out.tsv" ftype="tsv"/>
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158 <output name="similarity_matches" file="similarity/matches_test8_out.tsv" ftype="tsv"/>
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159 </test>
0
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160 </tests>
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161
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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162 <help>
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163 <![CDATA[
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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164 @HELP_matchms@
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165 ]]>
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166 </help>
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167
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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168 <citations>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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169 <citation type="doi">10.5281/zenodo.4589154</citation>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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170 <citation type="doi">10.21105/joss.02411</citation>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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171 </citations>
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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172 </tool>