Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate macros.xml @ 0:067a308223e3 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 10:18:24 +0000
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children 472dc85ce7c5
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067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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1 <macros>
067a308223e3 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>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="4.1.0">r-base</requirement>
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6 <requirement type="package" version="4.0.1">r-arrow</requirement>
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7 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
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8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
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9 </requirements>
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10 </xml>
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11
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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12 <xml name="creator">
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13 <creator>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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14 <person
067a308223e3 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"
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18 identifier="0000-0003-2056-8018" />
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19 <person
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20 givenName="Matej"
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21 familyName="Troják"
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22 url="https://github.com/xtrojak"
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23 identifier="0000-0003-0841-2707" />
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24 <person
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25 givenName="Martin"
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26 familyName="Čech"
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27 url="https://github.com/martenson"
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28 identifier="0000-0002-9318-1781" />
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29 <person
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30 givenName="Jiří"
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31 familyName="Novotný"
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32 url="https://github.com/xtracko"
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33 identifier="0000-0001-5449-3523" />
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34 <organization
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35 url="https://www.recetox.muni.cz/"
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36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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37 name="RECETOX MUNI"/>
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38 </creator>
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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." />
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45 <yield />
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46 </inputs>
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47 </xml>
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48
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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"
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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)." />
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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." />
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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." />
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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." />
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80 </section>
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81 </xml>
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diff changeset
82
067a308223e3 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">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
84 <section name="feature_detection" title="Feature detection">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
85 <param name="shape_model" type="select" display="radio"
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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.">
067a308223e3 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>
067a308223e3 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>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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parents:
diff changeset
90 </param>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
91 <param name="BIC_factor" type="float" value="2.0"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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92 label="BIC_factor"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
94 <param name="peak_estim_method" type="select" display="radio"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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95 label="peak_estim_method"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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96 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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97 <option value="moment" selected="true">Moment</option>
067a308223e3 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>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
99 </param>
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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101 label="min_bandwidth (optional)"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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102 help="The minimum bandwidth to use in the kernel smoother." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
103 <param name="max_bandwidth" type="float" optional="true"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
104 label="max_bandwidth (optional)"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
105 help="The maximum bandwidth to use in the kernel smoother." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
106 <param name="sd_cut_min" type="float" value="0.01"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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107 label="sd_cut_min"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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108 help="The minimum standard deviation of a feature to be not eliminated." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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109 <param name="sd_cut_max" type="float" value="500"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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110 label="sd_cut_max"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
111 help="The maximum standard deviation of a feature to be not eliminated." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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112 <param name="sigma_ratio_lim_min" type="float" value="0.01"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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113 label="sigma_ratio_lim_min"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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115 <param name="sigma_ratio_lim_max" type="float" value="100"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
116 label="sigma_ratio_lim_max"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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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." />
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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119 label="component_eliminate"
067a308223e3 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." />
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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122 label="moment_power"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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123 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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124 </section>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
125 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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126
067a308223e3 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">
067a308223e3 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">
067a308223e3 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"
067a308223e3 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)"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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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." />
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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133 label="align_mz_tol (optional)"
067a308223e3 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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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135 <param name="max_align_mz_diff" type="float" value="0.01"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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136 label="max_align_mz_diff"
067a308223e3 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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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138 </section>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
139 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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140
067a308223e3 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">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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142 <section name="weak_signal_recovery" title="Weak Signal Recovery">
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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144 label="recover_mz_range (optional)"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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146 <param name="recover_chr_range" type="float" optional="true"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
147 label="recover_chr_range (optional)"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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149 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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150 label="use_observed_range"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
151 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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152 <param name="recover_min_count" type="integer" value="3"
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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154 help="The minimum number of raw data points to be considered as a true feature." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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155 </section>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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156 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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157 <xml name="multibatch_processing">
067a308223e3 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">
067a308223e3 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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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160 label="minimum_batchwise_prop_detect"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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161 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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diff changeset
162 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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163 label="minimum_batch_prop"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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"
067a308223e3 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
067a308223e3 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.
067a308223e3 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." />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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184 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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 ${on_string}" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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190 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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197 <citation type="doi">10.1186/1471-2105-11-559</citation>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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198 <citation type="doi">10.1021/pr301053d</citation>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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202 </xml>
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203
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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204 <token name="@HELP_hybrid@">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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205 <![CDATA[
067a308223e3 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
067a308223e3 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
067a308223e3 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
067a308223e3 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 ]]>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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[
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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219 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
067a308223e3 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 ]]>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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224 </token>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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225
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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226 <token name="@HELP_two-step-hybrid@">
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227 <![CDATA[
067a308223e3 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
067a308223e3 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
067a308223e3 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.
067a308223e3 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
067a308223e3 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
067a308223e3 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
067a308223e3 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.
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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243 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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244 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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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>