Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate macros.xml @ 13:006736cab495 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author recetox
date Thu, 26 May 2022 16:44:17 +0000
parents e0f77e03599e
children 202ac259e077
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e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <macros>
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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2 <token name="@TOOL_VERSION@">0.9.4</token>
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e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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3 <xml name="requirements">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 <requirements>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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5 <requirement type="package" version="4.1.0">r-base</requirement>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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6 <requirement type="package" version="4.0.1">r-arrow</requirement>
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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7 <requirement type="package" version="0.9.4">r-recetox-aplcms</requirement>
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 </requirements>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 <xml name="creator">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 <creator>
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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14 <yield />
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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15 <person
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 givenName="Martin"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 familyName="Čech"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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18 url="https://github.com/martenson"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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19 identifier="0000-0002-9318-1781" />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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20 <person
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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21 givenName="Jiří"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 familyName="Novotný"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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23 url="https://github.com/xtracko"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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24 identifier="0000-0001-5449-3523" />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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25 <organization
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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26 url="https://www.recetox.muni.cz/"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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27 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 name="RECETOX MUNI"/>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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29 </creator>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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30 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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32 <xml name="inputs">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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33 <inputs>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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34 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 help="Mass spectrometry files for peak extraction." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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36 <yield />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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37 </inputs>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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38 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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39
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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40 <xml name="history_db">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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41 <param name="known_table" type="data" format="parquet" label="known_table"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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42 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)." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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43 <section name="history_db" title="Known-Table settings">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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44 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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45 help="The ppm tolerance to match identified features to known metabolites/features." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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47 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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48 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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49 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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50
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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51 <xml name="noise_filtering">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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52 <section name="noise_filtering" title="Noise filtering and peak detection">
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006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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53 <yield />
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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54 <param name="min_pres" type="float" value="0.5"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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55 label="min_pres"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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56 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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57 <param name="min_run" type="float" value="12"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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58 label="min_run"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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59 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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60 <param name="mz_tol" type="float" value="1e-05"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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61 label="mz_tol"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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62 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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63 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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64 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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65 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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66 label="baseline_correct_noise_percentile"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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67 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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68 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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69 label="intensity_weighted"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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70 help="Whether to weight the local density by signal intensities in initial peak detection." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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71 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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72 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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73
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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74 <xml name="feature_detection">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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75 <section name="feature_detection" title="Feature detection">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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76 <param name="shape_model" type="select" display="radio"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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77 label="shape_model"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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78 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.">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
79 <option value="Gaussian">Gaussian</option>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
80 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
81 </param>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
82 <param name="BIC_factor" type="float" value="2.0"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
83 label="BIC_factor"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
84 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
85 <param name="peak_estim_method" type="select" display="radio"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
86 label="peak_estim_method"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
87 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
88 <option value="moment" selected="true">Moment</option>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
89 <option value="EM">EM</option>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
90 </param>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
91 <param name="min_bandwidth" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
92 label="min_bandwidth (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
93 help="The minimum bandwidth to use in the kernel smoother." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
94 <param name="max_bandwidth" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
95 label="max_bandwidth (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
96 help="The maximum bandwidth to use in the kernel smoother." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
97 <param name="sd_cut_min" type="float" value="0.01"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
98 label="sd_cut_min"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
99 help="The minimum standard deviation of a feature to be not eliminated." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
100 <param name="sd_cut_max" type="float" value="500"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
101 label="sd_cut_max"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
102 help="The maximum standard deviation of a feature to be not eliminated." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
103 <param name="sigma_ratio_lim_min" type="float" value="0.01"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
104 label="sigma_ratio_lim_min"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
105 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
106 <param name="sigma_ratio_lim_max" type="float" value="100"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
107 label="sigma_ratio_lim_max"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
108 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
109 <param name="component_eliminate" type="float" value="0.01"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
110 label="component_eliminate"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
111 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
112 <param name="moment_power" type="float" value="1"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
113 label="moment_power"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
114 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
115 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
116 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
117
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
118 <xml name="peak_alignment">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
119 <section name="peak_alignment" title="Peak Alignment">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
120 <param name="align_chr_tol" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
121 label="align_chr_tol (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
122 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
123 <param name="align_mz_tol" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
124 label="align_mz_tol (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
125 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
126 <param name="max_align_mz_diff" type="float" value="0.01"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
127 label="max_align_mz_diff"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
128 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
129 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
130 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
131
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
132 <xml name="weak_signal_recovery">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
133 <section name="weak_signal_recovery" title="Weak Signal Recovery">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
134 <param name="recover_mz_range" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
135 label="recover_mz_range (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
136 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
137 <param name="recover_chr_range" type="float" optional="true"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
138 label="recover_chr_range (optional)"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
139 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." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
140 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
141 label="use_observed_range"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
142 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
143 <param name="recover_min_count" type="integer" value="3"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
144 label="recover_min_count"
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
145 help="The minimum number of raw data points to be considered as a true feature." />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
146 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
147 </xml>
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
148 <xml name="multibatch_processing">
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
149 <section name="multibatch_processing" title="Multibatch processing">
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
150 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
151 label="minimum_batchwise_prop_detect"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
152 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
153 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
154 label="minimum_batch_prop"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
155 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." />
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
156 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents: 11
diff changeset
157 label="batch_align_mz_tol"
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158 help="The m/z tolerance level for peak alignment within batch." />
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159 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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160 label="batch_align_chr_tol"
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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161 help="The retention time tolerance level for peak alignment within batch." />
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162 </section>
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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163 </xml>
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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164 <xml name="output_format">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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165 <section name="output_format" title="Output Format">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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166 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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167 </section>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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168 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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169
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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170 <xml name="unsupervised_outputs">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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171 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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172 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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173 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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174 <yield />
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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175 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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176
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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177 <xml name="citations">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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178 <citations>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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179 <citation type="doi">10.1093/bioinformatics/btp291</citation>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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180 <citation type="doi">10.1186/1471-2105-11-559</citation>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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181 <citation type="doi">10.1021/pr301053d</citation>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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182 <citation type="doi">10.1093/bioinformatics/btu430</citation>
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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183 <yield />
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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184 </citations>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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185 </xml>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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186
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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187 <token name="@HELP_hybrid@">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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188 <![CDATA[
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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189 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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190 detected features on the same machinery to help detect and quantify lower-intensity peaks.
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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191
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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192 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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193 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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194 technique, such as human serum.
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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195
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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196 @GENERAL_HELP@
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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197 ]]>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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198 </token>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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199
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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200 <token name="@HELP_unsupervised@">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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201 <![CDATA[
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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202 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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203 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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204
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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205 @GENERAL_HELP@
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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206 ]]>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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207 </token>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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208
13
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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diff changeset
209 <token name="@HELP_two-step-hybrid@">
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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diff changeset
210 <![CDATA[
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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211 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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diff changeset
212 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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213 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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214
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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215 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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diff changeset
216 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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217 technique, such as human serum.
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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218
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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219 @GENERAL_HELP@
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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220 ]]>
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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221 </token>
006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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222
11
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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223 <token name="@GENERAL_HELP@">
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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224 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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225 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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226 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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227 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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228 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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229 </token>
e0f77e03599e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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230 </macros>