Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate aplcms_hybrid.xml @ 1:30b1888f985a draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
author recetox
date Thu, 24 Sep 2020 00:16:24 +0000
parents 2bb3c7ae9777
children bb4ffaeba411
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30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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1 <tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy0">
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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2 <macros>
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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3 <import>aplcms_macros.xml</import>
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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4 </macros>
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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5
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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6 <expand macro="requirements" />
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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8 <command detect_errors="aggressive"><![CDATA[
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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9 #set file_str = str('", "').join([str($f) for $f in $files])
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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10
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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11 Rscript
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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12 -e 'x <- apLCMS::hybrid(
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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13 files = c("$file_str"),
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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14 known_table = rhdf5::h5read("$known_table", "aplcms_known_table"),
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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15 min_exp = $noise_filtering.min_exp,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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16 min_pres = $noise_filtering.min_pres,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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17 min_run = $noise_filtering.min_run,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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18 mz_tol = $noise_filtering.mz_tol,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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19 baseline_correct = $noise_filtering.baseline_correct,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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20 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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21 intensity_weighted = $noise_filtering.intensity_weighted,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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22 shape_model = "$feature_detection.shape_model",
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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23 BIC_factor = $feature_detection.BIC_factor,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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24 peak_estim_method = "$feature_detection.peak_estim_method",
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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25 min_bandwidth = $feature_detection.min_bandwidth,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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26 max_bandwidth = $feature_detection.max_bandwidth,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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27 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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28 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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29 component_eliminate = $feature_detection.component_eliminate,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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30 moment_power = $feature_detection.moment_power,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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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,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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34 match_tol_ppm = $history_db.match_tol_ppm,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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35 new_feature_min_count = $history_db.new_feature_min_count,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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36 recover_mz_range = $weak_signal_recovery.recover_mz_range,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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37 recover_chr_range = $weak_signal_recovery.recover_chr_range,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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38 use_observed_range = $weak_signal_recovery.use_observed_range,
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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39 recover_min_count = $weak_signal_recovery.recover_min_count
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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40 )'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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41 -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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42 -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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43 -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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44 -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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45 -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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46 -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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47 -e 'rhdf5::h5write(x\$updated_known_table, "$updated_known_table", "aplcms_known_table")'
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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48 ]]></command>
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49
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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50 <expand macro="inputs">
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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51 <expand macro="history_db" />
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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52 <expand macro="noise_filtering" />
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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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
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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58 <outputs>
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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59 <data name="peaks" format="h5" />
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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60 <data name="updated_known_table" format="h5" />
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61 </outputs>
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62
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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63 <help>
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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64 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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65 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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66
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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67 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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68 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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69 technique, such as human serum.
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70
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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71 @GENERAL_HELP@
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72 </help>
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73
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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74 <expand macro="citations" />
30b1888f985a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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75 </tool>