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annotate matchms_formatter.xml @ 11:803a430e9f0b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
author recetox
date Tue, 18 Oct 2022 13:20:25 +0000
parents 5c0e5344edf3
children 2f0545b02020
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1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.4" python_template_version="3.5">
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2 <description>reformat output tables of matchms</description>
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3
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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="@TOOL_VERSION@">matchms</requirement>
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11 <requirement type="package" version="1.1.4">pandas</requirement>
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12 <requirement type="package" version="8.0.1">click</requirement>
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13 </requirements>
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15 <environment_variables>
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16 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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17 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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18 </environment_variables>
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20 <command detect_errors="aggressive"><![CDATA[
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21 sh ${matchms_formatter_cli}
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22 ]]></command>
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24 <configfiles>
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25 <configfile name="matchms_formatter_cli">
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26 python3 ${__tool_directory__}/formatter.py \
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27 --sf "$scores" \
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28 --o "$output" \
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29 $method.selection \
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30 #if $method.selection == "get-thresholded-data"
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31 --st $method.scores_threshold \
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32 --mt $method.matches_threshold
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33 #else
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34 --k $method.k
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35 #end if
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36 </configfile>
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37 </configfiles>
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38
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39 <inputs>
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40 <param label="Scores object" name="scores" type="data" format="json" help="MatchMS Scores json file." />
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42 <conditional name="method">
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43 <param name="selection" type="select" label="Formatting method">
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44 <option value="get-thresholded-data" selected="true">Thresholding</option>
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45 <option value="get-top-k-data">Top K Matches</option>
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46 </param>
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47 <when value="get-thresholded-data">
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48 <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
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49 help="Threshold for matching score."/>
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50 <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
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51 help="Threshold for number of matches ions."/>
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52 </when>
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53 <when value="get-top-k-data">
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54 <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
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55 </when>
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56 </conditional>
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57
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58 </inputs>
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59 <outputs>
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60 <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv"/>
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61 </outputs>
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62
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63 <tests>
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64 <test>
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65 <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
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66 <param name="selection" value="get-thresholded-data"/>
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67 <param name="scores_threshold" value="0.4"/>
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68 <param name="matches_threshold" value="2"/>
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69 <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
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70 checksum="md5$db18b3f3dd5d8dea4db0fc1d59d3db3b"/>
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71 </test>
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72 <test>
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73 <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
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74 <param name="selection" value="get-top-k-data"/>
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75 <param name="k" value="3"/>
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76 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
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77 checksum="md5$ff827ec7413acac3d2394330935ace99"/>
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78 </test>
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79 </tests>
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80
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81 <help><![CDATA[
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82 @HELP_formatter@
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83 ]]></help>
2
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84 </tool>