Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate aplcms_hybrid.xml @ 0:2bb3c7ae9777 draft

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"planemo upload commit 40818fd30d8cf43485c215e7ce10c16757024957-dirty"
author recetox
date Tue, 25 Aug 2020 09:17:23 +0000
parents
children 30b1888f985a
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1 <tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" 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 $files])
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10
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11 Rscript
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12 -e 'result <- apLCMS::hybrid(
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13 files = c("$file_str"),
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14 known_table = arrow::read_feather("$known_table"),
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15 min_exp = $noise_filtering.min_exp,
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16 min_pres = $noise_filtering.min_pres,
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17 min_run = $noise_filtering.min_run,
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18 mz_tol = $noise_filtering.mz_tol,
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19 baseline_correct = $noise_filtering.baseline_correct,
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20 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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21 intensity_weighted = $noise_filtering.intensity_weighted,
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22 shape_model = "$feature_detection.shape_model",
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23 BIC_factor = $feature_detection.BIC_factor,
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24 peak_estim_method = "$feature_detection.peak_estim_method",
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25 min_bandwidth = $feature_detection.min_bandwidth,
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26 max_bandwidth = $feature_detection.max_bandwidth,
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27 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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28 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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29 component_eliminate = $feature_detection.component_eliminate,
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30 moment_power = $feature_detection.moment_power,
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31 align_chr_tol = $peak_alignment.align_chr_tol,
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32 align_mz_tol = $peak_alignment.align_mz_tol,
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33 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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34 match_tol_ppm = $history_db.match_tol_ppm,
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35 new_feature_min_count = $history_db.new_feature_min_count,
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36 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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37 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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38 use_observed_range = $weak_signal_recovery.use_observed_range,
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39 recover_min_count = $weak_signal_recovery.recover_min_count
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40 )'
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41 -e 'arrow::write_feather(result\$final_times, "$times")'
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42 -e 'arrow::write_feather(result\$final_features, "$features")'
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43 -e 'arrow::write_feather(result\$updated_known_table, "$updated_known_table")'
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44 -e 'arrow::write_feather(result\$aligned_times, "$aligned_times")'
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45 -e 'arrow::write_feather(result\$aligned_features, "$aligned_features")'
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46 -e 'arrow::write_feather(result\$corrected_features, "$corrected_features")'
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47 -e 'arrow::write_feather(result\$extracted_features, "$extracted_features")'
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48 ]]></command>
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49
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50 <expand macro="inputs">
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51 <expand macro="history_db" />
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52 <expand macro="noise_filtering" />
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53 <expand macro="feature_detection" />
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54 <expand macro="peak_alignment" />
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55 <expand macro="weak_signal_recovery" />
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56 </expand>
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57
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58 <outputs>
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59 <data name="times" format="time_table.feather" />
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60 <data name="features" format="peak_table.feather" />
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61 <data name="updated_known_table" format="aplcms_history.feather" />
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62 <data name="aligned_times" format="time_table.feather" hidden="true" />
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63 <data name="aligned_features" format="peak_table.feather" hidden="true" />
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64 <data name="corrected_features" format="peak_table.feather" hidden="true" />
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65 <data name="extracted_features" format="peak_table.feather" hidden="true" />
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66 </outputs>
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67
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68 <help>
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69 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
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70 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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71
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72 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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73 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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74 technique, such as human serum.
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75
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76 @GENERAL_HELP@
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77 </help>
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78
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79 <expand macro="citations" />
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80 </tool>