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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b974ff354fa375975050026482e1b6ded8005682
author recetox
date Thu, 08 Sep 2022 14:49:19 +0000
parents 60f34912b3de
children 574c6331e9db
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60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.3" python_template_version="3.5">
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2 <description>reformat output tables of matchms</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="8.0.1">click</requirement>
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12 </requirements>
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60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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14 <command detect_errors="aggressive"><![CDATA[
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15 sh ${matchms_formatter_cli}
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16 ]]></command>
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18 <configfiles>
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19 <configfile name="matchms_formatter_cli">
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20 python3 ${__tool_directory__}/formatter.py \
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21 --sf "$scores" \
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22 --mf "$matches" \
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23 --o "$output" \
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24 $method.selection \
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25 #if $method.selection == "get-thresholded-data"
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26 --st $method.scores_threshold \
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27 --mt $method.matches_threshold
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28 #else
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29 --k $method.k
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30 #end if
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31 </configfile>
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32 </configfiles>
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34 <inputs>
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35 <param label="Scores Table" name="scores" type="data" format="csv,tabular,tsv" help="Scores output table." />
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36 <param label="Matches Table" name="matches" type="data" format="csv,tabular,tsv" help="Scores output table." />
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39 <conditional name="method">
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40 <param name="selection" type="select" label="Formatting method">
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41 <option value="get-thresholded-data" selected="true">Thresholding</option>
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42 <option value="get-top-k-data">Top K Matches</option>
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43 </param>
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44 <when value="get-thresholded-data">
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45 <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
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46 help="Threshold for matching score."/>
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47 <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
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48 help="Threshold for number of matches ions."/>
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49 </when>
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50 <when value="get-top-k-data">
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51 <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
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52 </when>
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53 </conditional>
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54
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55 </inputs>
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56 <outputs>
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57 <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores"/>
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58 </outputs>
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59
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60 <tests>
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61 <test>
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62 <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
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63 <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
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64 <param name="selection" value="get-thresholded-data"/>
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65 <param name="scores_threshold" value="0.4"/>
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66 <param name="matches_threshold" value="2"/>
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67 <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
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68 checksum="md5$8929cdac47252da638f066261ffc16b7"/>
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69 </test>
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70 <test>
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71 <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
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72 <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
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73 <param name="selection" value="get-top-k-data"/>
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74 <param name="k" value="3"/>
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75 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
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76 checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81 Usage
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82 This tool creates user friendly tables from the data matrices produces by matchms.
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83 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
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84
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85 Input Table Format
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86 The tool expects two data matrices with the format as depicted below.
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87 The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
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88
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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89 +----------+------+------+-----+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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90 | | C001 | C002 | ... |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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91 +==========+======+======+=====+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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92 | Perylene | 0.1 | 0.0 | ... |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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93 +----------+------+------+-----+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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94 | Glycine | 0.5 | 0.34 | ... |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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95 +----------+------+------+-----+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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96 | ... | ... | ... | ... |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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97 +----------+------+------+-----+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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98
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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99 Output Table Format
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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100 +----------+-----------+---------+--------+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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101 | query | reference | matches | scores |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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102 +==========+===========+=========+========+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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103 | C001 | Glycine | 6 | 0.5 |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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104 +----------+-----------+---------+--------+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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105 | C002 | Glycine | 3 | 0.34 |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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106 +----------+-----------+---------+--------+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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107 | ... | ... | ... | ... |
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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108 +----------+-----------+---------+--------+
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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109
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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110 ]]></help>
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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111 </tool>