Mercurial > repos > recetox > recetox_aplcms_hybrid
annotate macros.xml @ 2:acd25e4fda77 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author | recetox |
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date | Fri, 10 Jun 2022 10:15:14 +0000 |
parents | 867c737a7f10 |
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rev | line source |
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0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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1 <macros> |
1
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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0
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2 <token name="@TOOL_VERSION@">0.9.4</token> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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3 <xml name="requirements"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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4 <requirements> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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5 <requirement type="package" version="4.1.0">r-base</requirement> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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6 <requirement type="package" version="4.0.1">r-arrow</requirement> |
2
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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7 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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8 <requirement type="package" version="1.0.7">r-dplyr</requirement> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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9 </requirements> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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10 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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11 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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12 <xml name="creator"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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13 <creator> |
2
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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14 <person |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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15 givenName="Maksym" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
1
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16 familyName="Skoryk" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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17 url="https://github.com/maximskorik" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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18 identifier="0000-0003-2056-8018" /> |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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19 <person |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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20 givenName="Matej" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
1
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21 familyName="Troják" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
1
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22 url="https://github.com/xtrojak" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
1
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23 identifier="0000-0003-0841-2707" /> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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24 <person |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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25 givenName="Martin" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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26 familyName="Čech" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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27 url="https://github.com/martenson" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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28 identifier="0000-0002-9318-1781" /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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29 <person |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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30 givenName="Jiří" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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31 familyName="Novotný" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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32 url="https://github.com/xtracko" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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33 identifier="0000-0001-5449-3523" /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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34 <organization |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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35 url="https://www.recetox.muni.cz/" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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37 name="RECETOX MUNI"/> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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38 </creator> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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39 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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40 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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41 <xml name="inputs"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
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42 <inputs> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
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43 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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44 help="Mass spectrometry files for peak extraction." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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45 <yield /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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46 </inputs> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
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47 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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48 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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49 <xml name="history_db"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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50 <param name="known_table" type="data" format="parquet" label="known_table" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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51 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
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52 <section name="history_db" title="Known-Table settings"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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53 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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54 help="The ppm tolerance to match identified features to known metabolites/features." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
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55 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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56 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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57 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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58 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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59 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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60 <xml name="noise_filtering"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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61 <section name="noise_filtering" title="Noise filtering and peak detection"> |
1
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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0
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62 <yield /> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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63 <param name="min_pres" type="float" value="0.5" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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64 label="min_pres" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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65 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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66 <param name="min_run" type="float" value="12" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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67 label="min_run" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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68 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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69 <param name="mz_tol" type="float" value="1e-05" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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70 label="mz_tol" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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71 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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72 <param name="baseline_correct" type="float" value="0" label="baseline_correct" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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73 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
74 <param name="baseline_correct_noise_percentile" type="float" value="0.05" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
75 label="baseline_correct_noise_percentile" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
76 help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
77 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
78 label="intensity_weighted" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
79 help="Whether to weight the local density by signal intensities in initial peak detection." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
80 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
81 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
82 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
83 <xml name="feature_detection"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
84 <section name="feature_detection" title="Feature detection"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
85 <param name="shape_model" type="select" display="radio" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
86 label="shape_model" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
87 help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better."> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
88 <option value="Gaussian">Gaussian</option> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
89 <option value="bi-Gaussian" selected="true">bi-Gaussian</option> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
90 </param> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
91 <param name="BIC_factor" type="float" value="2.0" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
92 label="BIC_factor" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
93 help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
94 <param name="peak_estim_method" type="select" display="radio" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
95 label="peak_estim_method" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
96 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM."> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
97 <option value="moment" selected="true">Moment</option> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
98 <option value="EM">EM</option> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
99 </param> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
100 <param name="min_bandwidth" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
101 label="min_bandwidth (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
102 help="The minimum bandwidth to use in the kernel smoother." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
103 <param name="max_bandwidth" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
104 label="max_bandwidth (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
105 help="The maximum bandwidth to use in the kernel smoother." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
106 <param name="sd_cut_min" type="float" value="0.01" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
107 label="sd_cut_min" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
108 help="The minimum standard deviation of a feature to be not eliminated." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
109 <param name="sd_cut_max" type="float" value="500" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
110 label="sd_cut_max" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
111 help="The maximum standard deviation of a feature to be not eliminated." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
112 <param name="sigma_ratio_lim_min" type="float" value="0.01" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
113 label="sigma_ratio_lim_min" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
114 help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
115 <param name="sigma_ratio_lim_max" type="float" value="100" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
116 label="sigma_ratio_lim_max" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
117 help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
118 <param name="component_eliminate" type="float" value="0.01" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
119 label="component_eliminate" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
120 help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
121 <param name="moment_power" type="float" value="1" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
122 label="moment_power" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
123 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
124 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
125 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
126 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
127 <xml name="peak_alignment"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
128 <section name="peak_alignment" title="Peak Alignment"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
129 <param name="align_chr_tol" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
130 label="align_chr_tol (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
131 help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
132 <param name="align_mz_tol" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
133 label="align_mz_tol (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
134 help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. The tolerance is given in absolute numbers, not scaled, i.e. for 10ppm tolerance enter '1e-05'. This value, multiplied by the m/z value, becomes the cutoff level." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
135 <param name="max_align_mz_diff" type="float" value="0.01" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
136 label="max_align_mz_diff" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
137 help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
138 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
139 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
140 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
141 <xml name="weak_signal_recovery"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
142 <section name="weak_signal_recovery" title="Weak Signal Recovery"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
143 <param name="recover_mz_range" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
144 label="recover_mz_range (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
145 help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
146 <param name="recover_chr_range" type="float" optional="true" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
|
147 label="recover_chr_range (optional)" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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148 help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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149 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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150 label="use_observed_range" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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151 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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152 <param name="recover_min_count" type="integer" value="3" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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153 label="recover_min_count" |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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154 help="The minimum number of raw data points to be considered as a true feature." /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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155 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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156 </xml> |
1
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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157 <xml name="multibatch_processing"> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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158 <section name="multibatch_processing" title="Multibatch processing"> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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159 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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160 label="minimum_batchwise_prop_detect" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
0
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161 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." /> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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0
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|
162 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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163 label="minimum_batch_prop" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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164 help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." /> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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165 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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166 label="batch_align_mz_tol" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
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167 help="The m/z tolerance level for peak alignment within batch." /> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
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168 <param name="batch_align_chr_tol" type="float" min="0" value="50.0" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
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169 label="batch_align_chr_tol" |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
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170 help="The retention time tolerance level for peak alignment within batch." /> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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171 </section> |
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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172 </xml> |
2
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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173 |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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174 <xml name="mz_tol_macro"> |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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175 <param name="mz_tol" type="float" value="1e-05" label="mz_tol" |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
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176 help="The m/z tolerance level for the grouping of data points. This value is expressed as the |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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177 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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178 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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179 For FTMS, 1e-5 is recommended." /> |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
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180 </xml> |
acd25e4fda77
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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181 |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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182 <xml name="output_format"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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183 <section name="output_format" title="Output Format"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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184 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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185 </section> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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186 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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187 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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188 <xml name="unsupervised_outputs"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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189 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" /> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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190 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" /> |
1
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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191 <yield /> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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192 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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193 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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|
194 <xml name="citations"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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195 <citations> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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196 <citation type="doi">10.1093/bioinformatics/btp291</citation> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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197 <citation type="doi">10.1186/1471-2105-11-559</citation> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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198 <citation type="doi">10.1021/pr301053d</citation> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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199 <citation type="doi">10.1093/bioinformatics/btu430</citation> |
1
867c737a7f10
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
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200 <yield /> |
0
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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201 </citations> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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202 </xml> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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203 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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204 <token name="@HELP_hybrid@"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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205 <![CDATA[ |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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206 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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207 detected features on the same machinery to help detect and quantify lower-intensity peaks. |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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208 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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209 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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210 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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211 technique, such as human serum. |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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212 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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213 @GENERAL_HELP@ |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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214 ]]> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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215 </token> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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216 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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217 <token name="@HELP_unsupervised@"> |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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218 <![CDATA[ |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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219 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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220 any historically detected features. For such functionality please use the Hybrid version of apLCMS. |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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221 |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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222 @GENERAL_HELP@ |
1633a2a34255
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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223 ]]> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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224 </token> |
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225 |
1
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226 <token name="@HELP_two-step-hybrid@"> |
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227 <![CDATA[ |
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228 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch |
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229 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and |
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230 historically detected features on the same machinery to help detect and quantify lower-intensity peaks. |
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231 |
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232 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography |
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233 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction |
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234 technique, such as human serum. |
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235 |
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236 @GENERAL_HELP@ |
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237 ]]> |
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238 </token> |
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239 |
0
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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240 <token name="@GENERAL_HELP@"> |
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241 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time |
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242 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise. |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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243 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time |
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244 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS |
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245 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/. |
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246 </token> |
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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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247 </macros> |