Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate recetox_aplcms_unsupervised.xml @ 9:b18c2d014b28 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 536b9620a22f25b2d2a909b6ec6b3681b2ec3970"
author recetox
date Tue, 05 Oct 2021 13:12:50 +0000
parents 6925295ae5c3
children 6057540f65a9
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6925295ae5c3 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 7b649938402c30227d8252d63e89a72f2f6fb628"
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1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy1">
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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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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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8 sh ${symlink_inputs} &&
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9 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
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10 ]]></command>
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11 <expand macro="creator" />
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12 <configfiles>
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13 <configfile name="symlink_inputs">
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14 #for $infile in $files
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15 ln -s '${infile}' '${infile.element_identifier}'
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16 #end for
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17 </configfile>
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18 <configfile name="run_script"><![CDATA[
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19 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
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21 unsupervised_main(
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22 sample_files = c('$filenames_str'),
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23 aligned_file = '${aligned_feature_sample_table}',
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24 recovered_file = '${recovered_feature_sample_table}',
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25 min_exp = $noise_filtering.min_exp,
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26 min_pres = $noise_filtering.min_pres,
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27 min_run = $noise_filtering.min_run,
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28 mz_tol = $noise_filtering.mz_tol,
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29 baseline_correct = $noise_filtering.baseline_correct,
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30 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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31 intensity_weighted = $noise_filtering.intensity_weighted,
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32 shape_model = '$feature_detection.shape_model',
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33 BIC_factor = $feature_detection.BIC_factor,
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34 peak_estim_method = '$feature_detection.peak_estim_method',
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35 min_bandwidth = $feature_detection.min_bandwidth,
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36 max_bandwidth = $feature_detection.max_bandwidth,
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37 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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38 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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39 component_eliminate = $feature_detection.component_eliminate,
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40 moment_power = $feature_detection.moment_power,
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41 align_chr_tol = $peak_alignment.align_chr_tol,
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42 align_mz_tol = $peak_alignment.align_mz_tol,
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43 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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44 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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45 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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46 use_observed_range = $weak_signal_recovery.use_observed_range,
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47 recover_min_count = $weak_signal_recovery.recover_min_count,
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48 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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49 )
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50 ]]></configfile>
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51 </configfiles>
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52
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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53 <expand macro="inputs">
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54 <expand macro="noise_filtering" />
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55 <expand macro="feature_detection" />
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56 <expand macro="peak_alignment" />
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57 <expand macro="weak_signal_recovery" />
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58 </expand>
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59
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60 <outputs>
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61 <expand macro="unsupervised_outputs" />
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
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67 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/>
4
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68 </test>
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69 </tests>
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70
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71 <help>
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72 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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73 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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74
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75 @GENERAL_HELP@
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76 </help>
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77
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78 <expand macro="citations" />
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79 </tool>