Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate recetox_aplcms_unsupervised.xml @ 4:1b9140057e5a 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 13:53:19 +0000
parents
children d06ec5e6721c
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1b9140057e5a "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_unsupervised" name="apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy0">
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2 <description>generate a feature table from LC/MS spectra</description>
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3 <macros>
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4 <import>recetox_aplcms_macros.xml</import>
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5 </macros>
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1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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7 <expand macro="requirements" />
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1b9140057e5a "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[
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10 sh ${symlink_inputs} &&
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11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
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12 ]]></command>
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1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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14 <configfiles>
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15 <configfile name="symlink_inputs">
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16 #for $infile in $files
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17 ln -s '${infile}' '${infile.element_identifier}'
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18 #end for
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19 </configfile>
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20 <configfile name="run_script"><![CDATA[
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21 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
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23 unsupervised_main(
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24 sample_files = c('$filenames_str'),
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25 aligned_file = '${aligned_feature_sample_table}',
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26 recovered_file = '${recovered_feature_sample_table}',
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27 min_exp = $noise_filtering.min_exp,
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28 min_pres = $noise_filtering.min_pres,
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29 min_run = $noise_filtering.min_run,
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30 mz_tol = $noise_filtering.mz_tol,
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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31 baseline_correct = $noise_filtering.baseline_correct,
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32 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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33 intensity_weighted = $noise_filtering.intensity_weighted,
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34 shape_model = '$feature_detection.shape_model',
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35 BIC_factor = $feature_detection.BIC_factor,
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36 peak_estim_method = '$feature_detection.peak_estim_method',
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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37 min_bandwidth = $feature_detection.min_bandwidth,
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38 max_bandwidth = $feature_detection.max_bandwidth,
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39 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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40 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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41 component_eliminate = $feature_detection.component_eliminate,
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42 moment_power = $feature_detection.moment_power,
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43 align_chr_tol = $peak_alignment.align_chr_tol,
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44 align_mz_tol = $peak_alignment.align_mz_tol,
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45 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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46 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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47 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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48 use_observed_range = $weak_signal_recovery.use_observed_range,
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49 recover_min_count = $weak_signal_recovery.recover_min_count,
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50 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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51 )
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52 ]]></configfile>
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53 </configfiles>
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54
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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55 <expand macro="inputs">
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56 <expand macro="noise_filtering" />
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57 <expand macro="feature_detection" />
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58 <expand macro="peak_alignment" />
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59 <expand macro="weak_signal_recovery" />
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60 </expand>
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61
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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62 <outputs>
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63 <expand macro="unsupervised_outputs" />
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64 </outputs>
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65
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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66 <tests>
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67 <test>
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68 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
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69 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet" compare="sim_size" delta="1000" />
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70 </test>
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71 </tests>
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72
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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73 <help>
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74 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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75 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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76
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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77 @GENERAL_HELP@
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78 </help>
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79
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80 <expand macro="citations" />
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81 </tool>