Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate macros.xml @ 11:ab2b7948bdb7 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:26:36 +0000
parents
children 5bb20231a48a
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11
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <macros>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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2 <token name="@TOOL_VERSION@">0.9.3</token>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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3 <xml name="requirements">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 <requirements>
ab2b7948bdb7 "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>
ab2b7948bdb7 "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>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement>
ab2b7948bdb7 "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>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 </requirements>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 <xml name="creator">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 <creator>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 <person
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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15 givenName="Martin"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 familyName="Čech"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 url="https://github.com/martenson"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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18 identifier="0000-0002-9318-1781" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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19 <person
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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20 givenName="Jiří"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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21 familyName="Novotný"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 url="https://github.com/xtracko"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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23 identifier="0000-0001-5449-3523" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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24 <organization
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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25 url="https://www.recetox.muni.cz/"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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26 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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27 name="RECETOX MUNI"/>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 </creator>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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29 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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30
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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31 <xml name="inputs">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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32 <inputs>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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33 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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34 help="Mass spectrometry files for peak extraction." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 <yield />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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36 </inputs>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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37 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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38
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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39 <xml name="history_db">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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40 <param name="known_table" type="data" format="parquet" label="known_table"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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41 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)." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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42 <section name="history_db" title="Known-Table settings">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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43 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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44 help="The ppm tolerance to match identified features to known metabolites/features." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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45 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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47 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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48 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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49
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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50 <xml name="noise_filtering">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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51 <section name="noise_filtering" title="Noise filtering and peak detection">
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52 <param name="min_exp" type="integer" min="1" value="2"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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53 label="min_exp"
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54 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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55 <param name="min_pres" type="float" value="0.5"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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56 label="min_pres"
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57 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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58 <param name="min_run" type="float" value="12"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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59 label="min_run"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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60 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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61 <param name="mz_tol" type="float" value="1e-05"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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62 label="mz_tol"
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63 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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64 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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65 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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66 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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67 label="baseline_correct_noise_percentile"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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68 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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69 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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70 label="intensity_weighted"
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71 help="Whether to weight the local density by signal intensities in initial peak detection." />
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72 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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73 </xml>
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74
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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75 <xml name="feature_detection">
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76 <section name="feature_detection" title="Feature detection">
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77 <param name="shape_model" type="select" display="radio"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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78 label="shape_model"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
79 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.">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
80 <option value="Gaussian">Gaussian</option>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
81 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
82 </param>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
83 <param name="BIC_factor" type="float" value="2.0"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
84 label="BIC_factor"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
85 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
86 <param name="peak_estim_method" type="select" display="radio"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
87 label="peak_estim_method"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
88 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
89 <option value="moment" selected="true">Moment</option>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
90 <option value="EM">EM</option>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
91 </param>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
92 <param name="min_bandwidth" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
93 label="min_bandwidth (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
94 help="The minimum bandwidth to use in the kernel smoother." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
95 <param name="max_bandwidth" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
96 label="max_bandwidth (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
97 help="The maximum bandwidth to use in the kernel smoother." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
98 <param name="sd_cut_min" type="float" value="0.01"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
99 label="sd_cut_min"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
100 help="The minimum standard deviation of a feature to be not eliminated." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
101 <param name="sd_cut_max" type="float" value="500"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
102 label="sd_cut_max"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
103 help="The maximum standard deviation of a feature to be not eliminated." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
104 <param name="sigma_ratio_lim_min" type="float" value="0.01"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
105 label="sigma_ratio_lim_min"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
106 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
107 <param name="sigma_ratio_lim_max" type="float" value="100"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
108 label="sigma_ratio_lim_max"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
109 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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diff changeset
110 <param name="component_eliminate" type="float" value="0.01"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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parents:
diff changeset
111 label="component_eliminate"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
112 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
113 <param name="moment_power" type="float" value="1"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
114 label="moment_power"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
115 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
116 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
117 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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diff changeset
118
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
119 <xml name="peak_alignment">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
120 <section name="peak_alignment" title="Peak Alignment">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
121 <param name="align_chr_tol" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
122 label="align_chr_tol (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
123 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
124 <param name="align_mz_tol" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
125 label="align_mz_tol (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
126 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
127 <param name="max_align_mz_diff" type="float" value="0.01"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
128 label="max_align_mz_diff"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
129 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
130 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
131 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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diff changeset
132
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
133 <xml name="weak_signal_recovery">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
134 <section name="weak_signal_recovery" title="Weak Signal Recovery">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
135 <param name="recover_mz_range" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
136 label="recover_mz_range (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
137 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
138 <param name="recover_chr_range" type="float" optional="true"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
139 label="recover_chr_range (optional)"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
140 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." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
141 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
142 label="use_observed_range"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
143 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
144 <param name="recover_min_count" type="integer" value="3"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
145 label="recover_min_count"
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
146 help="The minimum number of raw data points to be considered as a true feature." />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
147 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
148 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
149 <xml name="output_format">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
150 <section name="output_format" title="Output Format">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
151 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
152 </section>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
153 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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154
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
diff changeset
155 <xml name="unsupervised_outputs">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
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diff changeset
156 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents:
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157 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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158 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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159 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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160 </collection >
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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161 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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162 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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163 </collection >
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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164 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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165
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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166 <xml name="citations">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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167 <citations>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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168 <citation type="doi">10.1093/bioinformatics/btp291</citation>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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169 <citation type="doi">10.1186/1471-2105-11-559</citation>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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170 <citation type="doi">10.1021/pr301053d</citation>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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171 <citation type="doi">10.1093/bioinformatics/btu430</citation>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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172 </citations>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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173 </xml>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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174
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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175 <token name="@HELP_hybrid@">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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176 <![CDATA[
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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177 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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178 detected features on the same machinery to help detect and quantify lower-intensity peaks.
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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179
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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180 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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181 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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182 technique, such as human serum.
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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183
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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184 @GENERAL_HELP@
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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185 ]]>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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186 </token>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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187
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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188 <token name="@HELP_unsupervised@">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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189 <![CDATA[
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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190 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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191 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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192
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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193 @GENERAL_HELP@
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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194 ]]>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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195 </token>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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196
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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197 <token name="@GENERAL_HELP@">
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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198 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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199 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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200 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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201 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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202 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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203 </token>
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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204 </macros>