Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate recetox_aplcms_hybrid.xml @ 8:f22b38b72ac8 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 7b649938402c30227d8252d63e89a72f2f6fb628"
author recetox
date Thu, 19 Aug 2021 14:02:56 +0000
parents d1b2fafa8b79
children d62f052efae6
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f22b38b72ac8 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 7b649938402c30227d8252d63e89a72f2f6fb628"
recetox
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1 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy1">
4
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2 <description>generate a feature table from LC/MS spectra</description>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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3 <macros>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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4 <import>recetox_aplcms_macros.xml</import>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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5 </macros>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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6 <expand macro="requirements" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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7 <command detect_errors="aggressive"><![CDATA[
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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8 sh ${symlink_inputs} &&
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9 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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10 ]]></command>
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11 <expand macro="creator" />
4
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12 <configfiles>
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13 <configfile name="symlink_inputs">
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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14 #for $infile in $files
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15 ln -s '${infile}' '${infile.element_identifier}'
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16 #end for
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17 </configfile>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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18 <configfile name="run_script"><![CDATA[
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19 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
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20
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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21 hybrid_main(
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22 sample_files = c('$filenames_str'),
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23 known_table_file = '${known_table}',
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24 updated_known_table_file = '${updated_known_table}',
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25 pairing_file = '${feature_known_table_pairing}',
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26 aligned_file = '${aligned_feature_sample_table}',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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27 recovered_file = '${recovered_feature_sample_table}',
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28 min_exp = $noise_filtering.min_exp,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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29 min_pres = $noise_filtering.min_pres,
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30 min_run = $noise_filtering.min_run,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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31 mz_tol = $noise_filtering.mz_tol,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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32 baseline_correct = $noise_filtering.baseline_correct,
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33 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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34 intensity_weighted = $noise_filtering.intensity_weighted,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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35 shape_model = '$feature_detection.shape_model',
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36 BIC_factor = $feature_detection.BIC_factor,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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37 peak_estim_method = '$feature_detection.peak_estim_method',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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38 min_bandwidth = $feature_detection.min_bandwidth,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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39 max_bandwidth = $feature_detection.max_bandwidth,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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40 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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41 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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42 component_eliminate = $feature_detection.component_eliminate,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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43 moment_power = $feature_detection.moment_power,
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44 align_chr_tol = $peak_alignment.align_chr_tol,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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45 align_mz_tol = $peak_alignment.align_mz_tol,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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46 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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47 match_tol_ppm = $history_db.match_tol_ppm,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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48 new_feature_min_count = $history_db.new_feature_min_count,
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49 recover_mz_range = $weak_signal_recovery.recover_mz_range,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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50 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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51 use_observed_range = $weak_signal_recovery.use_observed_range,
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52 recover_min_count = $weak_signal_recovery.recover_min_count,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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53 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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54 )
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55 ]]></configfile>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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56 </configfiles>
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57
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58 <expand macro="inputs">
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59 <expand macro="history_db" />
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60 <expand macro="noise_filtering" />
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61 <expand macro="feature_detection" />
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62 <expand macro="peak_alignment" />
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63 <expand macro="weak_signal_recovery" />
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64 </expand>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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65
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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66 <outputs>
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67 <expand macro="unsupervised_outputs" />
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68 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" />
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69 <data name="feature_known_table_pairing" format="tabular" label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true" />
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70 </outputs>
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71
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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72 <tests>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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73 <test>
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74 <param name="known_table" value="known_table.parquet" ftype="parquet" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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75 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
7
d1b2fafa8b79 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 311863e9322de3e309361c51bcd1122212c8c050"
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76 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" compare="sim_size" delta="500" />
4
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77 </test>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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78 </tests>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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79
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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80 <help>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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81 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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82 detected features on the same machinery to help detect and quantify lower-intensity peaks.
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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83
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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84 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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85 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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86 technique, such as human serum.
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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87
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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88 @GENERAL_HELP@
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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89 </help>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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90
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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91 <expand macro="citations" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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92 </tool>