Mercurial > repos > recetox > aplcms_hybrid

annotate aplcms_hybrid.xml @ 3:2877bbac4c82 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ffadabe63b4a1428918cb80dc1f8598f41a458bd"
author recetox
date Mon, 17 May 2021 09:08:39 +0000
parents a1439454fe7f
children
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a1439454fe7f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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1 <tool id="aplcms_hybrid" name="apLCMS - Hybrid" 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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d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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8 <command detect_errors="aggressive"><![CDATA[
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9 Rscript ${run_script}
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10 ]]></command>
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a1439454fe7f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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12 <configfiles>
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13 <configfile name="run_script"><![CDATA[
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14 #set file_str = str("', '").join([str($f) for $f in $files])
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15
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16 x <- apLCMS::hybrid(
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17 files = c('$file_str'),
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18 known_table = apLCMS::load_known_table_from_hdf('$known_table'),
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19 min_exp = $noise_filtering.min_exp,
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20 min_pres = $noise_filtering.min_pres,
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21 min_run = $noise_filtering.min_run,
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22 mz_tol = $noise_filtering.mz_tol,
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23 baseline_correct = $noise_filtering.baseline_correct,
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24 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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25 intensity_weighted = $noise_filtering.intensity_weighted,
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26 shape_model = '$feature_detection.shape_model',
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27 BIC_factor = $feature_detection.BIC_factor,
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28 peak_estim_method = '$feature_detection.peak_estim_method',
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29 min_bandwidth = $feature_detection.min_bandwidth,
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30 max_bandwidth = $feature_detection.max_bandwidth,
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31 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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32 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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33 component_eliminate = $feature_detection.component_eliminate,
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34 moment_power = $feature_detection.moment_power,
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35 align_chr_tol = $peak_alignment.align_chr_tol,
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36 align_mz_tol = $peak_alignment.align_mz_tol,
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37 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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38 match_tol_ppm = $history_db.match_tol_ppm,
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39 new_feature_min_count = $history_db.new_feature_min_count,
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40 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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41 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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42 use_observed_range = $weak_signal_recovery.use_observed_range,
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43 recover_min_count = $weak_signal_recovery.recover_min_count,
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44 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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45 )
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46
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47 apLCMS::save_peaks_to_hdf('$peaks', x)
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48 apLCMS::save_known_table_to_hdf('$updated_known_table', x\$updated_known_table) ## NOTE the \ because we want cheetah to ignore the $ character
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49 ]]></configfile>
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50 </configfiles>
0
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51
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52 <expand macro="inputs">
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53 <expand macro="history_db" />
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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 <data name="peaks" format="h5" />
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62 <data name="updated_known_table" format="h5" />
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63 </outputs>
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65 <tests>
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66 <test>
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67 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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68 <param name="known_table" value="known_table.h5" ftype="h5"/>
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69 <output name="peaks" file="peaks_hybrid.h5" ftype="h5" compare="sim_size" delta="1000"/>
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70 </test>
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71 </tests>
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72
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73 <help>
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74 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
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75 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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76
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77 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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78 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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79 technique, such as human serum.
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80
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81 @GENERAL_HELP@
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82 </help>
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84 <expand macro="citations" />
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85 </tool>