Mercurial > repos > recetox > recetox_aplcms_remove_noise

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 5da5b5e8b95d93a24424155e5aebfbd337d2c4b6
author recetox
date Thu, 31 Oct 2024 11:23:50 +0000
parents ffbabefbd2e2
children
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1 <tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
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6 </macros>
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7 <expand macro="annotation"/>
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8 <edam_operations>
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9 <edam_operation>operation_3937</edam_operation>
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10 </edam_operations>
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11 <expand macro="refs"/>
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12 <expand macro="creator"/>
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13 <expand macro="requirements"/>
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15 <command detect_errors="aggressive"><![CDATA[
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16 python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
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17 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="run_script"><![CDATA[
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21 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
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22
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23 profile <- remove_noise(
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24 filename = '$input_file',
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25 min_pres = $min_pres,
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26 min_run = $min_run,
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27 mz_tol = ${mz_tol}/1e6,
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28 baseline_correct = $baseline_correct,
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29 baseline_correct_noise_percentile = 0.05,
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30 intensity_weighted = $intensity_weighted,
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31 do.plot = FALSE,
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32 cache = FALSE,
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33 grouping_threshold = $grouping_threshold
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34 )
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36 profile <- save_sample_name(profile, sample_name)
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37 save_data_as_parquet_file(profile, '$output_file')
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38 ]]></configfile>
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39 </configfiles>
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41 <inputs>
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42 <param label="Input spectra data" name="input_file" type="data" format="mzml"
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43 help="Sample data in .mzml format acquired in profile mode." />
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44 <expand macro="remove_noise_params"/>
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45 </inputs>
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47 <outputs>
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48 <data label="${($input_file.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" />
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49 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
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54 <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
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55 </test>
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56 <test>
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57 <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
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58 <param name="grouping_threshold" value="2" />
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59 <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
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60 </test>
0
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61 </tests>
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63 <help>
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64 <![CDATA[
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65 @REMOVE_NOISE_HELP@
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66
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67 @GENERAL_HELP@
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68 ]]>
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69 </help>
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70
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71 <expand macro="citations"/>
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72 </tool>