diff abims_xcms_xcmsSet.xml @ 26:626d3db664ef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf

--- a/abims_xcms_xcmsSet.xml	Thu Mar 02 08:20:04 2017 -0500
+++ b/abims_xcms_xcmsSet.xml	Wed Mar 22 16:04:45 2017 -0400
@@ -48,9 +48,8 @@
                 ## sigma "$methods.options_m.sigma"
                 max $methods.options_m.max
                 snthresh $methods.options_m.snthresh
-                ## mzdiff $methods.options_m.mzdiff
                 steps $methods.options_m.steps
-                ## sleep $methods.options_m.sleep
+                mzdiff $methods.options_m.mzdiff
             #end if
         #elif $methods.method == "MSW":
             snthr $methods.snthr
@@ -109,7 +108,7 @@
                     </param>
                     <when value="show">
                         <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
-                        <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " />
+                        <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" />
                         <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
                             <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
                             <option value="2">peak limits based on real data (more sensitive to noise)</option>
@@ -124,7 +123,7 @@
 
             <!-- matched Filter options -->
             <when value="matchedFilter">
-                <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" />
+                <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" />
                 <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" />
                 <conditional name="options_m">
                     <param name="option" type="select" label="Advanced options" >
@@ -132,15 +131,11 @@
                         <option value="hide" selected="true">hide</option>
                     </param>
                     <when value="show">
-<!--
-                        <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" />
--->
+                        <!--<param name="sigma" type="float" value="12.739935451" label="Standard deviation (width) of matched filtration model peak" help="[sigma] By default: fwhm/2.3548" />-->
                         <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
                         <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
                         <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" />
-<!--
-                        <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 " />
--->
+                        <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 " />
                     </when>
                     <when value="hide">
                     </when>
@@ -562,10 +557,12 @@
 Changelog/News
 --------------
 
-**Version 2.1.0 - 03/02/2017**
+**Version 2.1.0 - 22/02/2017**
 
 - 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".
 
+- 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
+
 **Version 2.0.11 - 22/12/2016**
 
 - BUGFIX: propose scanrange for all methods