Mercurial > repos > recetox > recetox_aplcms_unsupervised

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"planemo upload commit 40818fd30d8cf43485c215e7ce10c16757024957-dirty"
author recetox
date Tue, 25 Aug 2020 09:08:24 +0000
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children 52cec2e123fa
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1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@VERSION@">
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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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5
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6 <expand macro="requirements" />
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7
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8 <command detect_errors="aggressive"><![CDATA[
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9 #set file_str = str('", "').join([str($f) for $f in $files])
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10
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11 Rscript
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12 -e 'result <- apLCMS::unsupervised(
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13 files = c("$file_str"),
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14 min_exp = $noise_filtering.min_exp,
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15 min_pres = $noise_filtering.min_pres,
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16 min_run = $noise_filtering.min_run,
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17 mz_tol = $noise_filtering.mz_tol,
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18 baseline_correct = $noise_filtering.baseline_correct,
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19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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20 intensity_weighted = $noise_filtering.intensity_weighted,
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21 shape_model = "$feature_detection.shape_model",
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22 BIC_factor = $feature_detection.BIC_factor,
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23 peak_estim_method = "$feature_detection.peak_estim_method",
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24 min_bandwidth = $feature_detection.min_bandwidth,
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25 max_bandwidth = $feature_detection.max_bandwidth,
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26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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28 component_eliminate = $feature_detection.component_eliminate,
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29 moment_power = $feature_detection.moment_power,
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30 align_chr_tol = $peak_alignment.align_chr_tol,
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31 align_mz_tol = $peak_alignment.align_mz_tol,
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32 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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33 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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34 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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35 use_observed_range = $weak_signal_recovery.use_observed_range,
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36 recover_min_count = $weak_signal_recovery.recover_min_count
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37 )'
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38 -e 'arrow::write_feather(result\$final_times, "$times")'
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39 -e 'arrow::write_feather(result\$final_features, "$features")'
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40 -e 'arrow::write_feather(result\$aligned_times, "$aligned_times")'
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41 -e 'arrow::write_feather(result\$aligned_features, "$aligned_features")'
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42 -e 'arrow::write_feather(result\$corrected_features, "$corrected_features")'
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43 -e 'arrow::write_feather(result\$extracted_features, "$extracted_features")'
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44 ]]></command>
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45
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46 <expand macro="inputs">
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47 <expand macro="noise_filtering" />
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48 <expand macro="feature_detection" />
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49 <expand macro="peak_alignment" />
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50 <expand macro="weak_signal_recovery" />
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51 </expand>
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52
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53 <outputs>
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54 <data name="times" format="time_table.feather" />
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55 <data name="features" format="peak_table.feather" />
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56 <data name="aligned_times" format="time_table.feather" hidden="true" />
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57 <data name="aligned_features" format="peak_table.feather" hidden="true" />
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58 <data name="corrected_features" format="peak_table.feather" hidden="true" />
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59 <data name="extracted_features" format="peak_table.feather" hidden="true" />
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60 </outputs>
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61
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62 <help>
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63 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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64 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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65
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66 @GENERAL_HELP@
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67 </help>
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68
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69 <expand macro="citations" />
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70 </tool>