Mercurial > repos > recetox > matchms_formatter

annotate matchms_formatter.xml @ 3:e2a1dbeba196 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:23:30 +0000
parents 52abfe76c25b
children da32f57b4f88
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e2a1dbeba196 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <tool id="matchms_formatter" name="matchms output formatter" version="0.1.1" 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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0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
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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
0
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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,tsv" help="Scores output table."/>
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36 <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table."/>
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38 <conditional name="method">
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39 <param name="selection" type="select" label="Formatting method">
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40 <option value="get-thresholded-data" selected="true">Thresholding</option>
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41 <option value="get-top-k-data">Top K Matches</option>
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42 </param>
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43 <when value="get-thresholded-data">
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44 <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
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45 help="Threshold for matching score."/>
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46 <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
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47 help="Threshold for number of matches ions."/>
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48 </when>
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49 <when value="get-top-k-data">
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50 <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
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51 </when>
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52 </conditional>
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53
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54 </inputs>
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55 <outputs>
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56 <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores"/>
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
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62 <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
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63 <param name="selection" value="get-thresholded-data"/>
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64 <param name="scores_threshold" value="0.4"/>
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65 <param name="matches_threshold" value="2"/>
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66 <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
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67 checksum="md5$8929cdac47252da638f066261ffc16b7"/>
0
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68 </test>
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69 <test>
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70 <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
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71 <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
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72 <param name="selection" value="get-top-k-data"/>
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73 <param name="k" value="3"/>
3
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74 <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
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75 checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
0
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76 </test>
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77 </tests>
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78
3
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79 <help>
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80 <![CDATA[
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81 @HELP_formatter@
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82 ]]>
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83 </help>
2
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84 </tool>