Mercurial > repos > recetox > aplcms_unsupervised

annotate aplcms_unsupervised.xml @ 2:8c6dbef97001 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
author recetox
date Mon, 19 Apr 2021 12:26:57 +0000
parents bcc9f27fea2b
children
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8c6dbef97001 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy3">
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2 <macros>
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3 <import>aplcms_macros.xml</import>
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4 </macros>
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6 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 Rscript ${run_script}
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10 ]]></command>
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12 <configfiles>
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13 <configfile name="run_script"><![CDATA[
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14 #set file_str = str("', '").join([str($f) for $f in $files])
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16 x <- apLCMS::unsupervised(
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17 files = c('$file_str'),
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18 min_exp = $noise_filtering.min_exp,
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19 min_pres = $noise_filtering.min_pres,
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20 min_run = $noise_filtering.min_run,
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21 mz_tol = $noise_filtering.mz_tol,
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22 baseline_correct = $noise_filtering.baseline_correct,
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23 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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24 intensity_weighted = $noise_filtering.intensity_weighted,
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25 shape_model = '$feature_detection.shape_model',
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26 BIC_factor = $feature_detection.BIC_factor,
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27 peak_estim_method = '$feature_detection.peak_estim_method',
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28 min_bandwidth = $feature_detection.min_bandwidth,
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29 max_bandwidth = $feature_detection.max_bandwidth,
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30 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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31 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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32 component_eliminate = $feature_detection.component_eliminate,
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33 moment_power = $feature_detection.moment_power,
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34 align_chr_tol = $peak_alignment.align_chr_tol,
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35 align_mz_tol = $peak_alignment.align_mz_tol,
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36 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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37 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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38 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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39 use_observed_range = $weak_signal_recovery.use_observed_range,
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40 recover_min_count = $weak_signal_recovery.recover_min_count,
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41 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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42 )
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44 apLCMS::save_peaks_to_hdf('$peaks', x)
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45 ]]></configfile>
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46 </configfiles>
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48 <expand macro="inputs">
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49 <expand macro="noise_filtering" />
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50 <expand macro="feature_detection" />
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51 <expand macro="peak_alignment" />
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52 <expand macro="weak_signal_recovery" />
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53 </expand>
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55 <outputs>
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56 <data name="peaks" format="h5" />
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57 </outputs>
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59 <tests>
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60 <test>
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61 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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62 <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/>
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63 </test>
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64 </tests>
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66 <help>
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67 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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68 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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70 @GENERAL_HELP@
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71 </help>
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73 <expand macro="citations" />
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74 </tool>