Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate recetox_aplcms_hybrid.xml @ 4:c2213632ca71 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
author recetox
date Fri, 18 Jun 2021 13:54:00 +0000
parents
children 3a8864093eac
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c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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1 <tool id="recetox_aplcms_hybrid" name="apLCMS Hybrid" version="@TOOL_VERSION@+galaxy0">
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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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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c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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7 <expand macro="requirements" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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9 <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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10 sh ${symlink_inputs} &&
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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11 Rscript -e 'source("${__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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12 ]]></command>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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14 <configfiles>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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15 <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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16 #for $infile in $files
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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17 ln -s '${infile}' '${infile.element_identifier}'
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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18 #end for
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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19 </configfile>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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20 <configfile name="run_script"><![CDATA[
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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21 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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23 hybrid_main(
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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24 sample_files = c('$filenames_str'),
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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25 known_table_file = '${known_table}',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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26 updated_known_table_file = '${updated_known_table}',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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27 pairing_file = '${feature_known_table_pairing}',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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28 aligned_file = '${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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29 recovered_file = '${recovered_feature_sample_table}',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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30 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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31 min_pres = $noise_filtering.min_pres,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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32 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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33 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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34 baseline_correct = $noise_filtering.baseline_correct,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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35 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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36 intensity_weighted = $noise_filtering.intensity_weighted,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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37 shape_model = '$feature_detection.shape_model',
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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38 BIC_factor = $feature_detection.BIC_factor,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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39 peak_estim_method = '$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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40 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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41 max_bandwidth = $feature_detection.max_bandwidth,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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42 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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43 sigma_ratio_lim = c($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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44 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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45 moment_power = $feature_detection.moment_power,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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46 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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47 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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48 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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49 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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50 new_feature_min_count = $history_db.new_feature_min_count,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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51 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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52 recover_chr_range = $weak_signal_recovery.recover_chr_range,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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53 use_observed_range = $weak_signal_recovery.use_observed_range,
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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54 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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55 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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56 )
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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57 ]]></configfile>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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58 </configfiles>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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59
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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60 <expand macro="inputs">
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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61 <expand macro="history_db" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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62 <expand macro="noise_filtering" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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63 <expand macro="feature_detection" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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64 <expand macro="peak_alignment" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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65 <expand macro="weak_signal_recovery" />
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66 </expand>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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67
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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68 <outputs>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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69 <expand macro="unsupervised_outputs" />
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70 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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71 <data name="feature_known_table_pairing" format="tabular" label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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72 </outputs>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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73
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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74 <tests>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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75 <test>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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76 <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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77 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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78 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" compare="sim_size" delta="1000" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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79 </test>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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80 </tests>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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81
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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82 <help>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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83 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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84 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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85
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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86 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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87 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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88 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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89
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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90 @GENERAL_HELP@
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91 </help>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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92
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93 <expand macro="citations" />
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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94 </tool>