Mercurial > repos > recetox > matchms_formatter

annotate matchms_formatter.xml @ 29:6501d0287dcd draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4
author recetox
date Tue, 04 Jun 2024 07:13:22 +0000
parents 8bd942dcf1ad
children
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1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>reformat scores object of matchms to long format table</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>help.xml</import>
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7 </macros>
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8 <expand macro="creator"/>
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9 <edam_operations>
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10 <edam_operation>operation_0335</edam_operation>
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11 </edam_operations>
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12 <expand macro="bio.tools"/>
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14 <requirements>
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15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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16 <requirement type="package" version="1.1.4">pandas</requirement>
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17 </requirements>
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19 <command detect_errors="aggressive"><![CDATA[
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20 python3 '${formatter}'
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21 ]]></command>
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23 <environment_variables>
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24 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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25 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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26 <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable>
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27 <environment_variable name="RLIMIT_NPROC">4</environment_variable>
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28 </environment_variables>
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30 <configfiles>
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31 <configfile name="formatter">
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32 from matchms.importing import scores_from_json
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33 from pandas import DataFrame
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35 scores = scores_from_json('$scores')
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36 data = []
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38 for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)):
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39 data.append([scores.queries[col].metadata['$key'], scores.references[row].metadata['$key'], *scores.scores.data[i]])
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41 result = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names])
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43 result.to_csv('$output', sep="\t", index=False)
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44
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45 </configfile>
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46 </configfiles>
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48 <inputs>
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49 <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
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50 <param label="Key" name="key" type="text" value="compound_name" help="Name of the key to use. Default is 'compound_name'." />
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51 </inputs>
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52 <outputs>
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53 <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
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54 </outputs>
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56 <tests>
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57 <test>
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58 <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
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59 <param name="key" value="compound_name"/>
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60 <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
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61 checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
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62 </test>
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63 <test>
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64 <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
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65 <param name="key" value="compound_name"/>
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66 <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
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67 </test>
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68 </tests>
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69
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70 <help>
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71 @HELP_formatter@
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72 @HELP_matchms@
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73 </help>
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75 <citations>
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76 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
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77 </citations>
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78 </tool>