Mercurial > repos > recetox > aplcms_hybrid

annotate aplcms_hybrid.xml @ 0:d3d9ba599d51 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
author recetox
date Sun, 18 Oct 2020 10:36:05 +0000
parents
children 87f5cf0baf34
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d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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1 <tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy1">
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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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d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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 #set file_str = str('", "').join([str($f) for $f in $files])
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d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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11 Rscript
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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12 -e 'x <- apLCMS::hybrid(
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13 files = c("$file_str"),
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14 known_table = apLCMS::load_known_table_from_hdf("$known_table"),
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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15 min_exp = $noise_filtering.min_exp,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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16 min_pres = $noise_filtering.min_pres,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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20 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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 = $feature_detection.BIC_factor,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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24 peak_estim_method = "$feature_detection.peak_estim_method",
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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25 min_bandwidth = $feature_detection.min_bandwidth,
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26 max_bandwidth = $feature_detection.max_bandwidth,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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27 sd_cut = c($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),
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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29 component_eliminate = $feature_detection.component_eliminate,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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30 moment_power = $feature_detection.moment_power,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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31 align_chr_tol = $peak_alignment.align_chr_tol,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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32 align_mz_tol = $peak_alignment.align_mz_tol,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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33 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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,
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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39 recover_min_count = $weak_signal_recovery.recover_min_count
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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40 )'
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41 -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
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42 -e 'apLCMS::save_known_table_to_hdf("$updated_known_table", x\$updated_known_table)'
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43 ]]></command>
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44
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45 <expand macro="inputs">
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46 <expand macro="history_db" />
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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="peaks" format="h5" />
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55 <data name="updated_known_table" format="h5" />
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56 </outputs>
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58 <tests>
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59 <test>
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60 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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61 <param name="known_table" value="known_table.h5" ftype="h5"/>
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62 <output name="peaks" file="peaks_hybrid.h5" ftype="h5" compare="sim_size" delta="1000"/>
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63 </test>
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64 </tests>
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65
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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66 <help>
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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67 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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68 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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69
d3d9ba599d51 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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70 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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71 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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72 technique, such as human serum.
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73
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74 @GENERAL_HELP@
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75 </help>
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77 <expand macro="citations" />
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78 </tool>