Mercurial > repos > lecorguille > xcms_retcor
annotate abims_xcms_retcor.xml @ 16:d1d78a99ba28 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
author | lecorguille |
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date | Thu, 07 Mar 2019 07:41:34 -0500 |
parents | 950b97b679c6 |
children | 7faadba7c625 |
rev | line source |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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1 <tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@WRAPPER_VERSION@.0"> |
0 | 2 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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3 <description>Retention Time Correction</description> |
0 | 4 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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5 <macros> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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6 <import>macros.xml</import> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 <import>macros_xcms.xml</import> |
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8 </macros> |
0 | 9 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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10 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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11 <expand macro="stdio"/> |
0 | 12 |
1 | 13 <command><![CDATA[ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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14 @COMMAND_RSCRIPT@/xcms_retcor.r |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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15 image '$image' |
1 | 16 |
17 method $methods.method | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 #if $methods.method == "PeakGroups": |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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19 minFraction $methods.minFraction |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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20 extraPeaks $methods.extraPeaks |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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21 smooth $methods.smooth_cond.smooth |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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22 ## PeakGroupsSmoothLoess Advanced |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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24 family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family |
0 | 25 #else |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 binSize $methods.binSize |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 ## Advanced |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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28 #if $methods.ObiwarpAdv.centerSample != "": |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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29 centerSample $methods.ObiwarpAdv.centerSample |
0 | 30 #end if |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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31 response $methods.ObiwarpAdv.response |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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32 distFun $methods.ObiwarpAdv.distFunCond.distFun |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 gapInit $methods.ObiwarpAdv.distFunCond.gapInit |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 factorDiag $methods.ObiwarpAdv.factorDiag |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 factorGap $methods.ObiwarpAdv.factorGap |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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37 localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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38 initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty |
0 | 39 #end if |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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40 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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41 @COMMAND_FILE_LOAD@ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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42 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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43 @COMMAND_LOG_EXIT@ |
1 | 44 ]]></command> |
0 | 45 |
46 <inputs> | |
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47 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" /> |
0 | 48 <conditional name="methods"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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49 <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" > |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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50 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option> |
0 | 52 </param> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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53 <when value="PeakGroups"> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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54 <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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55 <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction" help="For a data set with 6 samples, ‘extraPeaks = 1’ uses all peak groups with a total peak count lower or equal to ‘6 + 1’. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" /> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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56 <conditional name="smooth_cond"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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57 <param argument="smooth" type="select" label="Smooth method" > |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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58 <option value="loess" selected="true">loess - non-linear alignment</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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59 <option value="linear">linear - linear alignment</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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60 </param> |
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61 <when value="loess"> |
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62 <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False"> |
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63 <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" /> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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64 <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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65 <option value="gaussian" selected="true">gaussian</option> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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66 <option value="symmetric">symmetric</option> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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67 </param> |
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68 </section> |
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69 </when> |
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70 <when value="linear" /> |
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71 </conditional> |
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72 </when> |
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73 <when value="Obiwarp"> |
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74 <param argument="binSize" type="float" value="1" label="Bin size (in mz dimension) to be used for the profile matrix generation" help="See ‘step’ parameter in ‘profile-matrix’ documentation for more details. (previously profStep)" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 <section name="ObiwarpAdv" title="Advanced Options" expanded="False"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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76 <param argument="centerSample" type="integer" value="" optional="true" label="Index of the center sample in the experiment" help="It defaults to ‘floor(median(1:length(fileNames(object))))’" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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77 <param argument="response" type="integer" value="1" label="Defining the responsiveness of warping" help="with ‘response = 0’ giving linear warping on start and end points and ‘response = 100’ warping using all bijective anchors." /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 <conditional name="distFunCond"> |
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79 <param argument="distFun" type="select" label="Distance function to be used"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80 <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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81 <option value="cor">cor - Pearson's correlation</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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82 <option value="cov">cov - covariance</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 <option value="prd">prd - product</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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84 <option value="euc">euc - Euclidian distance</option> |
1 | 85 </param> |
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86 <when value="cor_opt"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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87 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" /> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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88 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 </when> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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90 <when value="cor"> |
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91 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" /> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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92 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" /> |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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93 </when> |
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94 <when value="cov"> |
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95 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" /> |
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96 <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" /> |
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97 </when> |
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98 <when value="prd"> |
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99 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" /> |
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100 <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" /> |
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101 </when> |
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102 <when value="euc"> |
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103 <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" /> |
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104 <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" /> |
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105 </when> |
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106 </conditional> |
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107 <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" /> |
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108 <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" /> |
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109 <conditional name="localAlignmentCond"> |
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110 <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment"> |
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111 <option value="FALSE" selected="true">FALSE</option> |
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112 <option value="TRUE">TRUE</option> |
0 | 113 </param> |
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114 <when value="FALSE"> |
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115 <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" /> |
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116 </when> |
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117 <when value="TRUE"> |
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118 <param argument="initPenalty" type="float" value="0" label="Penalty for initiating an alignment" /> |
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119 </when> |
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120 </conditional> |
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121 </section> |
0 | 122 </when> |
123 </conditional> | |
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124 |
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125 <expand macro="input_file_load"/> |
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126 |
0 | 127 </inputs> |
128 | |
129 <outputs> | |
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130 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" /> |
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131 <data name="rawVSadjustedPdf" format="pdf" label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" /> |
0 | 132 </outputs> |
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133 |
0 | 134 <tests> |
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135 <test> |
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136 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/> |
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137 <conditional name="methods"> |
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138 <param name="method" value="PeakGroups"/> |
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139 <param name="extraPeaks" value="1"/> |
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140 <param name="minFraction" value="1"/> |
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141 <conditional name="smooth_cond"> |
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142 <param name="smooth" value="loess"/> |
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143 <section name="PeakGroupsSmoothLoessAdv"> |
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144 <param name="span" value="0.2"/> |
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145 <param name="family" value="gaussian"/> |
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146 </section> |
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147 </conditional> |
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148 </conditional> |
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149 <expand macro="test_file_load_single"/> |
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150 <assert_stdout> |
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151 <has_text text="extraPeaks: 1" /> |
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152 <has_text text="minFraction: 1" /> |
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153 <has_text text="span: 0.2" /> |
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154 <has_text text="object with 4 samples" /> |
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155 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" /> |
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156 <has_text text="Mass range: 200.1-600 m/z" /> |
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157 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
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158 <has_text text="Peak Groups: 0" /> |
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159 <has_text text="Sample classes: KO, WT" /> |
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160 </assert_stdout> |
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161 </test> |
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162 <!-- DISABLE FOR TRAVIS : Zip |
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163 <test> |
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164 <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/> |
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165 <conditional name="methods"> |
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166 <param name="method" value="PeakGroups"/> |
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167 <param name="extraPeaks" value="1"/> |
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168 <param name="minFraction" value="1"/> |
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169 <conditional name="smooth_cond"> |
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170 <param name="smooth" value="loess"/> |
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171 <section name="PeakGroupsSmoothLoessAdv"> |
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172 <param name="span" value="0.2"/> |
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173 <param name="family" value="gaussian"/> |
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174 </section> |
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175 </conditional> |
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176 </conditional> |
8
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177 <expand macro="test_file_load_zip"/> |
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178 <assert_stdout> |
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179 <has_text text="object with 4 samples" /> |
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180 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" /> |
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181 <has_text text="Mass range: 200.1-600 m/z" /> |
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182 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
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183 <has_text text="Peak Groups: 0" /> |
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184 <has_text text="Sample classes: KO, WT" /> |
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185 </assert_stdout> |
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186 </test> |
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187 --> |
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188 <!-- DISABLE FOR TRAVIS |
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189 Test to test the different methods parameters |
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190 <test> |
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191 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/> |
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192 <conditional name="methods"> |
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193 <param name="method" value="Obiwarp"/> |
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194 <section name="ObiwarpAdv"> |
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195 <param name="centerSample" value="1"/> |
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196 <param name="response" value="0"/> |
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197 <conditional name="distFunCond"> |
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198 <param name="distFun" value="cov"/> |
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199 <param name="gapInit" value="0.1" /> |
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200 </conditional> |
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201 </section> |
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202 </conditional> |
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203 <expand macro="test_file_load_single"/> |
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204 <assert_stdout> |
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205 <has_text text="centerSample: 1" /> |
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206 <has_text text="response: 0" /> |
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207 <has_text text="distFun: cov" /> |
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208 <has_text text="gapInit: 0.1" /> |
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209 <has_text text="gapExtend: 11.7" /> |
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210 </assert_stdout> |
0 | 211 </test> |
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212 --> |
0 | 213 </tests> |
214 | |
1 | 215 <help><![CDATA[ |
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216 |
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217 @HELP_AUTHORS@ |
0 | 218 |
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219 ================ |
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220 xcms adjustRtime |
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221 ================ |
0 | 222 |
223 ----------- | |
224 Description | |
225 ----------- | |
226 | |
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227 After matching peaks into groups, xcms can use those groups to identify and correct |
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228 correlated drifts in retention time from run to run. The aligned peaks can then be |
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229 used for a second pass of peak grouping which will be more accurate than the first. |
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230 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful |
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231 for identifying retention time drifts. Some groups may be missing peaks from a large |
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232 fraction of samples and thus provide an incomplete picture of the drift at that time point. |
0 | 233 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping. |
234 | |
235 .. class:: warningmark | |
236 | |
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237 **After an adjustRtime step, it is mandatory to do a groupChromPeaks step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is |
0 | 238 discarded)** |
239 | |
240 | |
241 | |
242 ----------------- | |
243 Workflow position | |
244 ----------------- | |
245 | |
246 | |
247 **Upstream tools** | |
248 | |
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249 ========================= ============================ ============================== |
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250 Name Output file Format |
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251 ========================= ============================ ============================== |
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252 xcms.findChromPeaks raw.xset.RData rdata.xcms.findchrompeaks |
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253 ------------------------- ---------------------------- ------------------------------ |
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254 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group |
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255 ========================= ============================ ============================== |
0 | 256 |
257 | |
258 **Downstream tools** | |
259 | |
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260 =========================== ============================ ================ |
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261 Name Output file Format |
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262 =========================== ============================ ================ |
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263 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group |
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264 =========================== ============================ ================ |
0 | 265 |
266 | |
267 **General schema of the metabolomic workflow** | |
268 | |
269 .. image:: xcms_retcor_workflow.png | |
270 | |
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271 --------------------------------------------------- |
0 | 272 |
273 ---------- | |
274 Parameters | |
275 ---------- | |
276 | |
277 Method | |
278 ------ | |
279 | |
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280 **PeakGroups** |
0 | 281 |
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282 | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample. |
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283 | See the PeakGroups_manual_ |
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284 |
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285 **Obiwarp** |
0 | 286 |
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287 | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping. |
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288 | See the Obiwarp_manual_ |
0 | 289 |
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290 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2 |
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291 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html |
0 | 292 |
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293 @HELP_XCMS_MANUAL@ |
0 | 294 |
295 ------------ | |
296 Output files | |
297 ------------ | |
298 | |
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299 xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format |
0 | 300 |
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301 | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow. |
0 | 302 |
1 | 303 |
304 --------------------------------------------------- | |
305 | |
306 Changelog/News | |
307 -------------- | |
308 | |
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309 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS |
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310 |
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311 **Version 3.4.4.0 - 08/02/2019** |
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312 |
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313 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) |
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314 |
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315 **Version 3.0.0.0 - 08/03/2018** |
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316 |
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317 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. |
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318 |
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319 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty) |
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320 |
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321 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values. |
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322 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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323 - CHANGE: removing of the TIC and BPC plots. You can now use the dedicated tool "xcms plot chromatogram" |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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324 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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325 |
9
e4e0254a3c0a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
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326 **Version 2.1.1 - 29/11/2017** |
e4e0254a3c0a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
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327 |
e4e0254a3c0a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
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328 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C |
e4e0254a3c0a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
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329 |
10
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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330 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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331 **Version 2.1.0 - 03/02/2017** |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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332 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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333 - IMPROVEMENT: xcms.retcor can deal with merged individual data |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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334 |
10
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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335 |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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336 **Version 2.0.8 - 22/12/2016** |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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337 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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338 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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339 |
10
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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340 |
6
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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341 **Version 2.0.7 - 06/07/2016** |
123824c7eaa8
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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342 |
123824c7eaa8
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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343 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
123824c7eaa8
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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344 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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345 |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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346 **Version 2.0.6 - 04/04/2016** |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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347 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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348 - TEST: refactoring to pass planemo test using conda dependencies |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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349 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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350 |
1 | 351 **Version 2.0.5 - 10/02/2016** |
352 | |
353 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
354 | |
355 - BUGFIX: some pdf remained empty even when the process succeed | |
356 | |
357 - UPDATE: refactoring of internal management of inputs/outputs | |
358 | |
359 - UPDATE: refactoring to feed the new report tool | |
360 | |
361 | |
362 **Version 2.0.2 - 02/06/2015** | |
363 | |
364 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
365 | |
366 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
367 | |
368 | |
369 ]]></help> | |
0 | 370 |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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371 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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372 <expand macro="citation" /> |
0 | 373 |
374 </tool> |