Mercurial > repos > recetox > recetox_aplcms_align_features

annotate macros.xml @ 0:e867e0c90d29 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:13:20 +0000
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children 4d1583e15960
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e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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1 <macros>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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2 <token name="@TOOL_VERSION@">0.9.4</token>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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3 <xml name="requirements">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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4 <requirements>
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5 <requirement type="package" version="4.1.0">r-base</requirement>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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6 <requirement type="package" version="4.0.1">r-arrow</requirement>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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7 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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9 </requirements>
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10 </xml>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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11
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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12 <xml name="creator">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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13 <creator>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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14 <person
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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15 givenName="Maksym"
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16 familyName="Skoryk"
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17 url="https://github.com/maximskorik"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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18 identifier="0000-0003-2056-8018" />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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19 <person
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20 givenName="Matej"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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21 familyName="Troják"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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22 url="https://github.com/xtrojak"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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23 identifier="0000-0003-0841-2707" />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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24 <person
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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25 givenName="Martin"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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26 familyName="Čech"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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27 url="https://github.com/martenson"
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28 identifier="0000-0002-9318-1781" />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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29 <person
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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30 givenName="Jiří"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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31 familyName="Novotný"
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32 url="https://github.com/xtracko"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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33 identifier="0000-0001-5449-3523" />
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34 <organization
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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35 url="https://www.recetox.muni.cz/"
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36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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37 name="RECETOX MUNI"/>
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38 </creator>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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39 </xml>
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40
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41 <xml name="inputs">
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42 <inputs>
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43 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
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44 help="Mass spectrometry files for peak extraction." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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45 <yield />
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46 </inputs>
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47 </xml>
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48
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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49 <xml name="history_db">
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50 <param name="known_table" type="data" format="parquet" label="known_table"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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51 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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52 <section name="history_db" title="Known-Table settings">
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53 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
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54 help="The ppm tolerance to match identified features to known metabolites/features." />
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55 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
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56 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
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57 </section>
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58 </xml>
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59
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60 <xml name="noise_filtering">
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61 <section name="noise_filtering" title="Noise filtering and peak detection">
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62 <yield />
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63 <param name="min_pres" type="float" value="0.5"
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64 label="min_pres"
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65 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
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66 <param name="min_run" type="float" value="12"
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67 label="min_run"
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68 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
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69 <param name="mz_tol" type="float" value="1e-05"
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70 label="mz_tol"
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71 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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72 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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73 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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74 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
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75 label="baseline_correct_noise_percentile"
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76 help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." />
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77 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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78 label="intensity_weighted"
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79 help="Whether to weight the local density by signal intensities in initial peak detection." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
80 </section>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
81 </xml>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
82
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
83 <xml name="feature_detection">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
84 <section name="feature_detection" title="Feature detection">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
85 <param name="shape_model" type="select" display="radio"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
86 label="shape_model"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
87 help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better.">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
88 <option value="Gaussian">Gaussian</option>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
89 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
90 </param>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
91 <param name="BIC_factor" type="float" value="2.0"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
92 label="BIC_factor"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
93 help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
94 <param name="peak_estim_method" type="select" display="radio"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
95 label="peak_estim_method"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
96 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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97 <option value="moment" selected="true">Moment</option>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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98 <option value="EM">EM</option>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
99 </param>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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100 <param name="min_bandwidth" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
101 label="min_bandwidth (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
102 help="The minimum bandwidth to use in the kernel smoother." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
103 <param name="max_bandwidth" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
104 label="max_bandwidth (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
105 help="The maximum bandwidth to use in the kernel smoother." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
106 <param name="sd_cut_min" type="float" value="0.01"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
107 label="sd_cut_min"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
108 help="The minimum standard deviation of a feature to be not eliminated." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
109 <param name="sd_cut_max" type="float" value="500"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
110 label="sd_cut_max"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
111 help="The maximum standard deviation of a feature to be not eliminated." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
112 <param name="sigma_ratio_lim_min" type="float" value="0.01"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
113 label="sigma_ratio_lim_min"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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114 help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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115 <param name="sigma_ratio_lim_max" type="float" value="100"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
116 label="sigma_ratio_lim_max"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
117 help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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118 <param name="component_eliminate" type="float" value="0.01"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
119 label="component_eliminate"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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120 help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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121 <param name="moment_power" type="float" value="1"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
122 label="moment_power"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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123 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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124 </section>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
125 </xml>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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126
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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127 <xml name="peak_alignment">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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128 <section name="peak_alignment" title="Peak Alignment">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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129 <param name="align_chr_tol" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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130 label="align_chr_tol (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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131 help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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132 <param name="align_mz_tol" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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133 label="align_mz_tol (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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134 help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. The tolerance is given in absolute numbers, not scaled, i.e. for 10ppm tolerance enter '1e-05'. This value, multiplied by the m/z value, becomes the cutoff level." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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135 <param name="max_align_mz_diff" type="float" value="0.01"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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136 label="max_align_mz_diff"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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137 help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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138 </section>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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139 </xml>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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140
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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141 <xml name="weak_signal_recovery">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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142 <section name="weak_signal_recovery" title="Weak Signal Recovery">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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143 <param name="recover_mz_range" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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144 label="recover_mz_range (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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145 help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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146 <param name="recover_chr_range" type="float" optional="true"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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147 label="recover_chr_range (optional)"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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148 help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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149 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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150 label="use_observed_range"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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151 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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152 <param name="recover_min_count" type="integer" value="3"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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153 label="recover_min_count"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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154 help="The minimum number of raw data points to be considered as a true feature." />
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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155 </section>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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156 </xml>
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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157 <xml name="multibatch_processing">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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158 <section name="multibatch_processing" title="Multibatch processing">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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159 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
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160 label="minimum_batchwise_prop_detect"
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161 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
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162 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
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163 label="minimum_batch_prop"
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164 help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." />
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165 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
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166 label="batch_align_mz_tol"
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167 help="The m/z tolerance level for peak alignment within batch." />
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168 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
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169 label="batch_align_chr_tol"
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170 help="The retention time tolerance level for peak alignment within batch." />
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171 </section>
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172 </xml>
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173
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174 <xml name="mz_tol_macro">
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175 <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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176 help="The m/z tolerance level for the grouping of data points. This value is expressed as the
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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177 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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178 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6.
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179 For FTMS, 1e-5 is recommended." />
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180 </xml>
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181
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182 <xml name="output_format">
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183 <section name="output_format" title="Output Format">
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184 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
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185 </section>
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186 </xml>
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187
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188 <xml name="unsupervised_outputs">
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189 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
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190 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
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191 <yield />
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192 </xml>
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193
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194 <xml name="citations">
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195 <citations>
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196 <citation type="doi">10.1093/bioinformatics/btp291</citation>
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197 <citation type="doi">10.1186/1471-2105-11-559</citation>
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198 <citation type="doi">10.1021/pr301053d</citation>
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199 <citation type="doi">10.1093/bioinformatics/btu430</citation>
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200 <yield />
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201 </citations>
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202 </xml>
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203
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204 <token name="@HELP_hybrid@">
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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205 <![CDATA[
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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206 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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207 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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208
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209 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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210 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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211 technique, such as human serum.
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212
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213 @GENERAL_HELP@
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214 ]]>
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215 </token>
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216
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217 <token name="@HELP_unsupervised@">
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218 <![CDATA[
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219 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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220 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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221
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222 @GENERAL_HELP@
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223 ]]>
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224 </token>
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225
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226 <token name="@HELP_two-step-hybrid@">
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227 <![CDATA[
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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228 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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229 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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230 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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231
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232 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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233 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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234 technique, such as human serum.
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235
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236 @GENERAL_HELP@
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237 ]]>
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238 </token>
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239
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240 <token name="@GENERAL_HELP@">
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241 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
e867e0c90d29 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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242 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
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243 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
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244 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
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245 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
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246 </token>
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247 </macros>