Mercurial > repos > marie-tremblay-metatoul > nmr_preprocessing
annotate NmrPreprocessing_xml.xml @ 2:5e64657b4fe5 draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
author | lecorguille |
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date | Wed, 28 Mar 2018 08:05:12 -0400 |
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2
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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1 <tool id="NMR_Preprocessing" name="NMR_Preprocessing" version="@WRAPPER_VERSION@"> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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2 <description> Preprocessing of 1D NMR spectra </description> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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3 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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4 <macros> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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5 <import>macros.xml</import> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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6 </macros> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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7 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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8 <expand macro="requirements"> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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9 <requirement type="package" version="1.9_12">r-ptw</requirement> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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10 <requirement type="package" version="1.2_12">r-matrix</requirement> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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11 </expand> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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12 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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13 <expand macro="stdio"/> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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14 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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15 <command> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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16 ## Wrapper |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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17 Rscript $__tool_directory__/NmrPreprocessing_wrapper.R |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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18 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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19 ## Data matrix of FID spectra |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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20 dataMatrixFid $dataMatrixFid |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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21 ## Sample metadata matrix |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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22 sampleMetadataFid $sampleMetadataFid |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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23 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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24 ## First order phase correction |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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25 ## Graphical display |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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26 FirstOPCGraph $GDC.FirstOPCGraph |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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27 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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28 ## Water and / or solvents suppression |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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29 ## Smoothing parameter |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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30 lambda $SS.lambda |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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31 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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32 ## Graphical display |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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33 SSGraph $SS.SSGraph |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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34 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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35 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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36 ## Apodization |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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37 ## Graphical display |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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38 ApodGraph $Apod.ApodGraph |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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39 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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40 apodizationMethod $Apod.apodizationMethod.method |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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41 #if $Apod.apodizationMethod.method == "exp": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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42 ## Line broadening for the exponential window |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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43 expLB $Apod.apodizationMethod.expLB |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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44 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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45 #if $Apod.apodizationMethod.method == "cos2": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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46 ## Phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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47 phase $Apod.apodizationMethod.phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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48 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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49 #if $Apod.apodizationMethod.method == "hanning": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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50 ## Phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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51 phase $Apod.apodizationMethod.phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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52 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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53 #if $Apod.apodizationMethod.method == "hamming": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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54 ## Phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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55 phase $Apod.apodizationMethod.phase |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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56 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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57 #if $Apod.apodizationMethod.method == "blockexp": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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58 ## Proportion of signal in the window |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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59 rectRatio $Apod.apodizationMethod.rectRatio |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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60 expLB $Apod.apodizationMethod.expLB |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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61 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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62 #if $Apod.apodizationMethod.method == "blockcos2": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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63 ## Proportion of signal in the window |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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64 rectRatio $Apod.apodizationMethod.rectRatio |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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65 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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66 #if $Apod.apodizationMethod.method == "gauss": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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67 ## Line broadening for the gaussian window |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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68 gaussLB $Apod.apodizationMethod.gaussLB |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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69 #end if |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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70 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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71 ## Fourier transform |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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72 ## Graphical display |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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73 FTGraph $FT.FTGraph |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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74 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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75 ## Zero order phase correction |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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76 ## Graphical display |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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77 ZeroOPCGraph $ZOPC.ZeroOPCGraph |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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78 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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79 zeroOrderPhaseMethod $ZOPC.zeroOrderPhaseMethod |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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80 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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81 excludeZoneZeroPhase.choice ${ZOPC.excludeZoneZeroPhase.choice} |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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82 #if str($ZOPC.excludeZoneZeroPhase.choice) == "YES": |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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83 #for $i in $ZOPC.excludeZoneZeroPhase.conditions: |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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84 excludeZoneZeroPhase_left ${i.excludeZoneZeroPhase_left} |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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85 excludeZoneZeroPhase_right ${i.excludeZoneZeroPhase_right} |
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86 #end for |
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87 #end if |
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88 |
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89 ## Shift referencing |
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90 ## Graphical display |
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91 SRGraph $SR.SRGraph |
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92 |
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93 ## Definition of the search zone |
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94 shiftReferencingRange $SR.shiftReferencingRange.method |
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95 #if $SR.shiftReferencingRange.method == "nearvalue": |
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96 pctNearValue $SR.shiftReferencingRange.pctNearValue |
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97 #end if |
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98 #if $SR.shiftReferencingRange.method == "window": |
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99 #for $i in $SR.shiftReferencingRange.conditions: |
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100 shiftReferencingRangeLeft ${i.shiftReferencingRangeLeft} |
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101 shiftReferencingRangeRight ${i.shiftReferencingRangeRight} |
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102 #end for |
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103 #end if |
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104 shiftHandling $SR.shiftHandling |
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105 ppmvalue $SR.ppmvalue |
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106 |
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107 ## Baseline correction |
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108 ## Graphical display |
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109 BCGraph $BC.BCGraph |
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110 |
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111 lambdaBc $BC.lambdaBc |
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112 pBc $BC.pBc |
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113 epsilon $BC.epsilon |
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114 |
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115 excludeZoneBC.choice ${BC.excludeZoneBC.choice} |
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116 #if str($BC.excludeZoneBC.choice) == "YES": |
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117 #for $i in $BC.excludeZoneBC.conditions: |
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118 excludeZoneBC_left ${i.excludeZoneBC_left} |
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119 excludeZoneBC_right ${i.excludeZoneBC_right} |
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120 #end for |
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121 #end if |
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122 |
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123 |
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124 ## sets negative intensities to zero |
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125 NegativetoZero $NZ.NegativetoZero |
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126 |
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127 ## final spectra |
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128 ## Graphical display |
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129 FinalGraph $FinalGraph |
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130 |
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131 |
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132 ## Outputs |
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133 dataMatrix $dataMatrix |
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134 variableMetadata $variableMetadata |
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135 graphOut $graphOut |
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136 logOut $logOut |
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137 |
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138 </command> |
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139 |
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140 <inputs> |
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141 <param name="dataMatrixFid" type="data" label="Data matrix of FIDs" help="" format="tabular" /> |
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142 <param name="sampleMetadataFid" type="data" label="Sample metadata matrix" help="" format="tabular" /> |
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143 |
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144 <section name="GDC" title="Group Delay Correction" expanded="true"> |
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145 <param name="FirstOPCGraph" label="Display the FIDs after 1st order phase correction?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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146 <option value="NO"> NO </option> |
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147 <option value="YES"> YES </option> |
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148 </param> |
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149 </section> |
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150 |
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151 <section name="SS" title="Solvent Suppression" expanded="true"> |
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152 <param name="lambda" label="Solvent Suppression: Smoothing parameter" type="float" value="1000000" help="Default value is 1e6"/> |
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153 |
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154 <param name="SSGraph" label="Display the FIDs after solvent suppression?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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155 <option value="NO"> NO </option> |
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156 <option value="YES"> YES </option> |
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157 </param> |
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158 </section> |
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159 |
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160 |
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161 <section name="Apod" title="Apodization" expanded="true"> |
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162 <conditional name="apodizationMethod" > |
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163 <param name="method" label="Apodization: method" type="select" help="Default method is Decreasing Exponential signal. See details below" > |
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164 <option value="exp" /> |
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165 <option value="cos2" /> |
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166 <option value="hanning" /> |
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167 <option value="hamming" /> |
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168 <option value="blockexp" /> |
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169 <option value="blockcos2" /> |
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170 <option value="gauss" /> |
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171 </param> |
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172 <when value="exp"> |
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173 <param name="expLB" type="float" label="Line broadening" value="1" help="Default value is 1" /> |
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174 </when> |
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175 <when value="cos2"> |
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176 <param name="phase" type="float" label="Phase" value="0" help="Default value is 0" /> |
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177 </when> |
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178 <when value="hanning"> |
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179 <param name="phase" type="float" label="Phase" value="0" help="Default value is 0" /> |
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180 </when> |
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181 <when value="hamming"> |
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182 <param name="phase" type="float" label="Phase" value="0" help="Default value is 0" /> |
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183 </when> |
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184 <when value="blockexp"> |
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185 <param name="rectRatio" type="float" label="Proportion of signal in the window" value="0.5" help="Default value is 0.5" /> |
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186 <param name="expLB" type="float" label="Line broadening" value="1" help="Default value is 1" /> |
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187 </when> |
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188 <when value="blockcos2"> |
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189 <param name="rectRatio" type="float" label="Proportion of signal in the window" value="0.5" help="Default value is 0.5" /> |
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190 </when> |
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191 <when value="gauss"> |
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192 <param name="gaussLB" type="float" label="Line broadening" value="0.3" help="Default value is 0.3" /> |
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193 </when> |
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194 </conditional> |
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195 |
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196 <param name="ApodGraph" label="Display the FIDs after Apodization?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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197 <option value="NO"> NO </option> |
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198 <option value="YES"> YES </option> |
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199 </param> |
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200 </section> |
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201 |
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202 <section name="FT" title="Fourier Transform" expanded="true"> |
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203 <param name="FTGraph" label="Display the Fourier transformed spectra?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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204 <option value="NO"> NO </option> |
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205 <option value="YES"> YES </option> |
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206 </param> |
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207 </section> |
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208 |
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209 <section name="ZOPC" title="Zero Order Phase Correction" expanded="true"> |
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210 <param name="zeroOrderPhaseMethod" type="select" label="Zero Order Phase Correction: method" help="Method used to select the angles to rotate the spectra" > |
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211 <option value="rms" selected="yes"> rms </option> |
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212 <option value="max" > max </option> |
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213 </param> |
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214 <conditional name="excludeZoneZeroPhase"> |
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215 <param name="choice" type="select" label="Zero Order Phase Correction: exclusion area(s)" help="Choose if you want to exclude particular zone(s)" > |
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216 <option value="YES" selected="true" > YES </option> |
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217 <option value="NO" > NO </option> |
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218 </param> |
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219 <when value="YES"> |
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220 <repeat name="conditions" title="Exclusion_zone" min="1"> |
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221 <param name="excludeZoneZeroPhase_left" label="Excusion zone: left border" type="float" value="5.1" /> |
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222 <param name="excludeZoneZeroPhase_right" label="Excusion zone: right border" type="float" value="4.5" /> |
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223 </repeat> |
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224 </when> |
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225 <when value="NO"> |
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226 </when> |
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227 </conditional> |
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228 |
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229 <param name="ZeroOPCGraph" label="Display the spectra after the Zero Order Phase Correction?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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230 <option value="NO"> NO </option> |
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231 <option value="YES"> YES </option> |
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232 </param> |
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233 </section> |
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234 |
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235 <section name="SR" title="Shift Referencing" expanded="true"> |
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236 <conditional name="shiftReferencingRange" > |
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237 <param name="method" label="Shift Referencing: definition of the search zone" type="select" help="Definition of the search zone" > |
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238 <option value="nearvalue" /> |
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239 <option value="all" /> |
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240 <option value="window" /> |
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241 </param> |
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242 |
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243 <when value="all" /> |
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244 <when value="nearvalue"> |
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245 <param name="pctNearValue" type="float" label="percentage of the ppm axis around the ppm value to look for the reference compound peak" value="0.02" help="Default value is 0.02" /> |
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246 </when> |
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247 <when value="window"> |
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248 <repeat name="conditions" title="Search_zone"> |
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249 <param name="shiftReferencingRangeLeft" label="Search zone: left border" type="float" value="1" /> |
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250 <param name="shiftReferencingRangeRight" label="Search zone: right border" type="float" value="-1" /> |
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251 </repeat> |
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252 </when> |
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253 </conditional> |
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254 |
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255 <param name="shiftHandling" type="select" label="Shift Referencing: shiftHandling" help="How to deal with shifts between spectra on their left and right sides" > |
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256 <option value="zerofilling" selected="yes"> zerofilling </option> |
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257 <option value="cut" > cut </option> |
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258 <option value="circular" > circular </option> |
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259 </param> |
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260 |
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261 <param name="ppmvalue" type="float" label="Shift Referencing: the value of the reference peak in ppm" value="0" help="Default value is 0" /> |
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262 |
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263 <param name="SRGraph" label="Display the spectra after Shift Referencing?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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264 <option value="NO"> NO </option> |
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265 <option value="YES"> YES </option> |
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266 </param> |
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267 </section> |
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268 |
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269 |
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270 <section name="BC" title="Baseline Correction" expanded="true"> |
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271 <param name="lambdaBc" type="float" label="Baseline Correction: smoothing parameter" value="100000.0" help="Smoothing parameter, generally 1e5 – 1e8. Default value is 100000" /> |
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272 <param name="pBc" type="float" label="Baseline Correction: asymmetry parameter" value="0.05" help="Asymmetry parameter. Default value is 0.05" /> |
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273 <param name="epsilon" type="float" label="Baseline Correction: numerical precision for convergence when estimating the baseline" value="0.00000001" help="Numerical precision for convergence when estimating the baseline. Default value is 1e-8" /> |
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274 |
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275 <conditional name="excludeZoneBC"> |
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276 <param name="choice" type="select" label="Baseline Correction: exclusion area(s)" help="Choose if you want to exclude particular zone(s)" > |
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277 <option value="YES" > YES </option> |
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278 <option value="NO" selected="true" > NO </option> |
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279 </param> |
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280 <when value="YES"> |
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281 <repeat name="conditions" title="Exclusion_zone" min="1"> |
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282 <param name="excludeZoneBC_left" label="Excusion zone: left border" type="float" value="5.1" /> |
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283 <param name="excludeZoneBC_right" label="Excusion zone: right border" type="float" value="4.5" /> |
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284 </repeat> |
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285 </when> |
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286 <when value="NO"> |
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287 </when> |
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288 </conditional> |
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289 |
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290 <param name="BCGraph" label="Display the spectra after Baseline Correction?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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291 <option value="NO"> NO </option> |
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292 <option value="YES"> YES </option> |
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293 </param> |
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294 </section> |
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295 |
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296 <section name="NZ" title="Negative intensities to Zero" expanded="true"> |
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297 <param name="NegativetoZero" label="Set negative intensities to zero?" type="select" help="If YES, sets negative intensities to zero"> |
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298 <option value="NO"> NO </option> |
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299 <option value="YES" selected="yes"> YES </option> |
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300 </param> |
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301 </section> |
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302 |
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303 <param name="FinalGraph" label="Display the final spectra?" type="select" help="Select 'YES' to display the spectra or 'NO' to not display them "> |
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304 <option value="YES"> YES </option> |
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305 <option value="NO"> NO </option> |
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306 </param> |
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307 |
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308 </inputs> |
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309 |
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310 <outputs> |
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311 <data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" /> |
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312 <data format="tabular" name="variableMetadata" label="${tool.name}_variableMetadata" /> |
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313 <data format="txt" name="logOut" label="${tool.name}_log" /> |
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314 <data format="pdf" name="graphOut" label="${tool.name}_graph" /> |
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315 </outputs> |
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316 |
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317 |
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318 <tests> |
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319 <test> |
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320 <param name="dataMatrixFid" value="NMR_ReadFids_dataMatrix.tabular"/> |
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321 <param name="sampleMetadataFid" value="sampleMetadata.tabular"/> |
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322 <section name="GDC"> |
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323 <param name="FirstOPCGraph" value="NO"/> |
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324 </section> |
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325 <section name="SS"> |
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326 <param name="lambda" value="1000000" /> |
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327 <param name="SSGraph" value="NO"/> |
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328 </section> |
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329 <section name="Apod"> |
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330 <conditional name="apodizationMethod"> |
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331 <param name="method" value="exp" /> |
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332 <param name="expLB" value="1" /> |
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333 </conditional> |
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334 <param name="ApodGraph" value="NO"/> |
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335 </section> |
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336 <section name="FT"> |
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337 <param name="FTGraph" value="NO"/> |
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338 </section> |
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339 <section name="ZOPC"> |
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340 <param name="zeroOrderPhaseMethod" value="rms" /> |
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341 <conditional name="excludeZoneZeroPhase" > |
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342 <param name="choice" value="YES" /> |
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343 <param name="conditions_0|excludeZoneZeroPhase_left" value="5.1" /> |
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344 <param name="conditions_0|excludeZoneZeroPhase_right" value="4.5" /> |
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345 </conditional> |
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346 <param name="ZeroOPCGraph" value="NO"/> |
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347 </section> |
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348 <section name="SR"> |
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349 <conditional name="shiftReferencingRange"> |
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350 <param name="method" value="nearvalue"/> |
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351 <param name="pctNearValue" value="0.02"/> |
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352 </conditional> |
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353 <param name="shiftHandling" value= "zerofilling"/> |
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354 <param name="ppmvalue" value="0" /> |
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355 <param name="SRGraph" value="NO"/> |
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356 </section> |
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357 <section name="BC"> |
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358 <param name="lambdaBc" value="100000.0" /> |
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359 <param name="pBc" value="0.05" /> |
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360 <param name="epsilon" value="0.00000001"/> |
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361 <param name="BCGraph" value="NO"/> |
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362 </section> |
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363 <section name="NZ"> |
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364 <param name="NegativetoZero" value="YES" /> |
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365 </section> |
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366 <param name="FinalGraph" value="YES" /> |
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367 <output name="dataMatrix" value="NMR_Preprocessing_dataMatrix.tabular" /> |
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368 </test> |
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369 </tests> |
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370 |
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371 <help> |
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372 |
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373 @HELP_AUTHORS@ |
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374 |
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375 |
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376 ===================== |
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377 Spectra preprocessing |
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378 ===================== |
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379 |
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380 ----------- |
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381 Description |
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382 ----------- |
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383 |
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384 These steps correspond to the following steps in the PEPS-NMR R library (https://github.com/ManonMartin/PEPSNMR): |
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385 |
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386 * Group Delay suppression (First order phase correction) |
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387 * Removal of solvent residuals signal from the FID |
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388 * Apodization to increase the Signal-to-Noise ratio of the FID |
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389 * Fourier transformation |
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390 * Zero order phase correction |
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391 * Shift referencing to calibrate the spectra with internal compound referencing |
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392 * Baseline correction |
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393 * Setting of negatives values to 0 |
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394 |
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395 |
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396 ----------------- |
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397 Workflow position |
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398 ----------------- |
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399 |
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400 **Upstream tools** |
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401 |
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402 +---------------------------+-------------------------+--------+ |
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403 | Name | Output file | Format | |
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404 +===========================+=========================+========+ |
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405 |NMR_Read | NMR_Read_dataMatrix | Tabular| |
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406 +---------------------------+-------------------------+--------+ |
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407 |NMR_Read | NMR_Read_sampleMetadata | Tabular| |
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408 +---------------------------+-------------------------+--------+ |
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409 |
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410 |
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411 |
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412 **Downstream tools** |
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413 |
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414 +---------------------------+----------------------+--------+ |
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415 | Name | Output file | Format | |
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416 +===========================+======================+========+ |
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417 |NMR_Alignement | dataMatrix | Tabular| |
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418 +---------------------------+----------------------+--------+ |
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419 |NMR_Bucketing | dataMatrix | Tabular| |
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420 +---------------------------+----------------------+--------+ |
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421 |Normalization | dataMatrix | Tabular| |
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422 +---------------------------+----------------------+--------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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423 |Univariate | variableMetadata | Tabular| |
5e64657b4fe5
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424 +---------------------------+----------------------+--------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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425 |Multivariate | sampleMetadata | Tabular| |
5e64657b4fe5
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426 +---------------------------+----------------------+--------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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427 | | variableMetadata | Tabular| |
5e64657b4fe5
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428 +---------------------------+----------------------+--------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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429 |
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430 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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431 ----------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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432 Input files |
5e64657b4fe5
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433 ----------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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434 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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435 +--------------------------------+-----------------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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436 | File | Format | |
5e64657b4fe5
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437 +================================+=================+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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438 |1 : dataMatrix | tabular | |
5e64657b4fe5
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439 +--------------------------------+-----------------+ |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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440 |2 : sampleMetadata | tabular | |
5e64657b4fe5
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441 +--------------------------------+-----------------+ |
5e64657b4fe5
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442 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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443 **dataMatrix file** |
5e64657b4fe5
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444 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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445 sample x variable matrix with tabular separations and "." as decimal; the table must not contain metadata apart from row and column names; the row names must be identical to the rownames of the sample metadata. |
5e64657b4fe5
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446 |
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447 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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448 **sampleMetadata file** |
5e64657b4fe5
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449 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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450 sample x metadata matrix with tabular separations and "." as decimal for numeric metadata and NA for missing values. |
5e64657b4fe5
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451 |
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452 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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453 ---------------------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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454 Steps parameters |
5e64657b4fe5
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455 ---------------------- |
5e64657b4fe5
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456 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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457 **Solvent Suppression** |
5e64657b4fe5
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458 ----------------------------------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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459 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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460 **Smoothing parameter** lambda: The higher lambda is, the smoother the estimated solvent signal will be |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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461 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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462 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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463 **Apodization** |
5e64657b4fe5
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464 ---------------------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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465 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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466 The **types of apodization** are: |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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467 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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468 * exp: The signal is multiplied by a decreasing exponential exp(-t/LineBroadening). |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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469 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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470 * cos2: The signal is multiplied by the value of a cosinus squared from 0 (where its value is 1) until pi/2 (where its value is 0). |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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471 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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472 * blockexp: The first part of the signal (described by the proportion of signal in the window) is left unchanged and the second is multiplied by exp(-t/LineBroadening) starting at value 1. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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473 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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474 * blockcos2: The first part is left unchanged as with blockexp and the second part is multiplied by a cosinus squared where its value starts at 1 at the end of the block and ends at 0 at the end of the signal. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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475 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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476 * gauss: The signal is multiplied by a gaussian window centered at the beginning of the FID and with sigma=1/LineBroadening. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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477 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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478 * hanning: The signal is multiplied by a hanning window : 0.5 + 0.5 cos. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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479 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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480 * hamming: The signal is multiplied by a hamming window : 0.54 + 0.46 cos. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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481 |
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482 |
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483 |
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484 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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485 **Zero Order Phase Correction** |
5e64657b4fe5
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486 ----------------------------------- |
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487 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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488 **Zero Order Phase correction method**: |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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489 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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490 * rms: A positiveness criterion is applied on the spectrum with a quantile probability parameter to trim the values. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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491 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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492 * max: Optimization of the maximal spectral intensity. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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493 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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494 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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495 **Exclusion area(s) for the Zero Order Phase Correction**: enables to optimize the criterion with excluded spectral window(s), by default the water region is excluded. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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496 |
5e64657b4fe5
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497 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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498 **Shift Referencing** |
5e64657b4fe5
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499 ---------------------- |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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500 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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501 The **searching window** can be adapted: |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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502 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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503 * nearvalue: the search concentrates around the value of the reference peak in ppm. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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504 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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505 * all: search accross the whole ppm axis. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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506 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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507 * window: the search is operated in the windows defined by the Search_zone bounds. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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|
508 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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509 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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510 **shiftHandling**: spectra can be shifted differently, we can handle misalignment of the left and right of the spectrum by different ways: |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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511 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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512 * zerofilling: The extremities at which a spectrum is not defined are replaced by 0. It makes sense since in practice the spectrum is close to zero at the extremities. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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513 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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514 * NAfilling: The extremities at which a spectrum is not defined are replaced by NA. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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515 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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516 * circular: The spectra are shifted circularly which means that the end of a spectrum is reproduced at the beginning. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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517 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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518 * cut: The ppm values for which some spectra are not defined are removed. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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519 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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520 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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521 **value of the reference peak**: the value in ppm of the reference peak. By default the value is 0 ppm. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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522 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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523 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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524 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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525 **Baseline Correction** |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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526 ---------------------------- |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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527 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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528 **Smoothing parameter**: the larger it is, the smoother the estimated baseline will be. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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529 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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530 **Asymmetry parameter**: the smaller it is, the less the estimated baseline will try to follow peaks when it is under the spectrum and the more it will try to be under the spectrum. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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531 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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532 **numerical precision**: numerical precision for convergence when estimating the baseline. |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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533 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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534 **Exclusion area(s) for the Baseline Correction**: enables to optimize the criterion with excluded spectral window(s), by default the water region is excluded. |
5e64657b4fe5
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535 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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536 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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537 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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538 **Negative intensities to Zero** |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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539 ------------------------------------ |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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540 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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541 **Set negative intensities to zero**: the set of negative intensities to zero is optional. |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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542 |
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543 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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544 ------------ |
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545 Output files |
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546 ------------ |
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547 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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548 NMR_Preprocessing_dataMatrix |
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549 | tabular output |
5e64657b4fe5
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550 | Data matrix with n rows (descriptors) and p columns (samples) containing the preprocessed spectra. |
5e64657b4fe5
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551 | |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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552 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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553 NMR_Preprocessing_variableMetadata |
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554 | tabular output |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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555 | Data matrix with 1 row (ppm value) and p columns (descriptors). |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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556 | |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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557 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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558 NMR_Preprocessing_log |
5e64657b4fe5
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559 | text output |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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560 | Contains warnings and the input parameters |
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561 | |
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562 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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563 NMR_Preprocessing_graph.pdf |
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564 | pdf output |
5e64657b4fe5
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565 | line plots of preprocessed spectra |
5e64657b4fe5
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566 | |
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567 |
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568 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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569 @HELP_CHANGELOG@ |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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570 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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571 </help> |
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572 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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573 <expand macro="citation" /> |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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574 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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575 </tool> |