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annotate matchms_formatter.xml @ 22:f76a397afbe1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b797ce0fea5cb3d9a0cf0ec31a21f9b73f112b4e
author recetox
date Mon, 15 Jan 2024 12:25:49 +0000
parents f7718efde4d5
children 402620029a7a
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1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy3" 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="8.0.1">click</requirement>
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17 <requirement type="package" version="1.1.4">pandas</requirement>
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18 </requirements>
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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 <environment_variables>
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25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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26 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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27 <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable>
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28 <environment_variable name="RLIMIT_NPROC">4</environment_variable>
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29 </environment_variables>
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31 <configfiles>
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32 <configfile name="matchms_formatter_cli">
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33 python3 ${__tool_directory__}/formatter.py \
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34 --sf '$scores' \
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35 --o '$output'
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36 </configfile>
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37 </configfiles>
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39 <inputs>
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40 <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
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41 </inputs>
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42 <outputs>
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43 <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
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44 </outputs>
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46 <tests>
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47 <test>
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48 <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
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49 <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
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50 checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
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51 </test>
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52 <test>
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53 <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
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54 <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
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55 </test>
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56 </tests>
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57
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58 <help>
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59 @HELP_formatter@
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60 @HELP_matchms@
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61 </help>
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63 <citations>
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64 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
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65 </citations>
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66 </tool>