Mercurial > repos > lecorguille > xcms_xcmsset
comparison abims_xcms_xcmsSet.xml @ 26:626d3db664ef draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
| author | lecorguille |
|---|---|
| date | Wed, 22 Mar 2017 16:04:45 -0400 |
| parents | dc4d3e2b9968 |
| children | b90e4f92e8b5 |
comparison
equal
deleted
inserted
replaced
| 25:dc4d3e2b9968 | 26:626d3db664ef |
|---|---|
| 46 fwhm $methods.fwhm | 46 fwhm $methods.fwhm |
| 47 #if $methods.options_m.option == "show": | 47 #if $methods.options_m.option == "show": |
| 48 ## sigma "$methods.options_m.sigma" | 48 ## sigma "$methods.options_m.sigma" |
| 49 max $methods.options_m.max | 49 max $methods.options_m.max |
| 50 snthresh $methods.options_m.snthresh | 50 snthresh $methods.options_m.snthresh |
| 51 ## mzdiff $methods.options_m.mzdiff | |
| 52 steps $methods.options_m.steps | 51 steps $methods.options_m.steps |
| 53 ## sleep $methods.options_m.sleep | 52 mzdiff $methods.options_m.mzdiff |
| 54 #end if | 53 #end if |
| 55 #elif $methods.method == "MSW": | 54 #elif $methods.method == "MSW": |
| 56 snthr $methods.snthr | 55 snthr $methods.snthr |
| 57 nearbyPeak $methods.nearbyPeak | 56 nearbyPeak $methods.nearbyPeak |
| 58 winSize.noise $methods.winSize_noise | 57 winSize.noise $methods.winSize_noise |
| 107 <option value="show">show</option> | 106 <option value="show">show</option> |
| 108 <option value="hide" selected="true">hide</option> | 107 <option value="hide" selected="true">hide</option> |
| 109 </param> | 108 </param> |
| 110 <when value="show"> | 109 <when value="show"> |
| 111 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> | 110 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> |
| 112 <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " /> | 111 <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap" /> |
| 113 <param name="integrate" type="select" label="peak limits method" help="[integrate]" > | 112 <param name="integrate" type="select" label="peak limits method" help="[integrate]" > |
| 114 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> | 113 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> |
| 115 <option value="2">peak limits based on real data (more sensitive to noise)</option> | 114 <option value="2">peak limits based on real data (more sensitive to noise)</option> |
| 116 </param> | 115 </param> |
| 117 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> | 116 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> |
| 122 </conditional> | 121 </conditional> |
| 123 </when> | 122 </when> |
| 124 | 123 |
| 125 <!-- matched Filter options --> | 124 <!-- matched Filter options --> |
| 126 <when value="matchedFilter"> | 125 <when value="matchedFilter"> |
| 127 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> | 126 <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> |
| 128 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> | 127 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> |
| 129 <conditional name="options_m"> | 128 <conditional name="options_m"> |
| 130 <param name="option" type="select" label="Advanced options" > | 129 <param name="option" type="select" label="Advanced options" > |
| 131 <option value="show">show</option> | 130 <option value="show">show</option> |
| 132 <option value="hide" selected="true">hide</option> | 131 <option value="hide" selected="true">hide</option> |
| 133 </param> | 132 </param> |
| 134 <when value="show"> | 133 <when value="show"> |
| 135 <!-- | 134 <!--<param name="sigma" type="float" value="12.739935451" label="Standard deviation (width) of matched filtration model peak" help="[sigma] By default: fwhm/2.3548" />--> |
| 136 <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" /> | |
| 137 --> | |
| 138 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> | 135 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> |
| 139 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> | 136 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> |
| 140 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> | 137 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> |
| 141 <!-- | 138 <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " /> |
| 142 <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " /> | |
| 143 --> | |
| 144 </when> | 139 </when> |
| 145 <when value="hide"> | 140 <when value="hide"> |
| 146 </when> | 141 </when> |
| 147 </conditional> | 142 </conditional> |
| 148 </when> | 143 </when> |
| 560 --------------------------------------------------- | 555 --------------------------------------------------- |
| 561 | 556 |
| 562 Changelog/News | 557 Changelog/News |
| 563 -------------- | 558 -------------- |
| 564 | 559 |
| 565 **Version 2.1.0 - 03/02/2017** | 560 **Version 2.1.0 - 22/02/2017** |
| 566 | 561 |
| 567 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". | 562 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". |
| 563 | |
| 564 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 | |
| 568 | 565 |
| 569 **Version 2.0.11 - 22/12/2016** | 566 **Version 2.0.11 - 22/12/2016** |
| 570 | 567 |
| 571 - BUGFIX: propose scanrange for all methods | 568 - BUGFIX: propose scanrange for all methods |
| 572 | 569 |