# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1399648078 -7200
# Node ID b1015b9241cdb014f2fca9bd51ffffef5368df6c
# Parent  ecd3f6c9e6061a7ca9e1f87be7ef6b11de8c91da
Added option for using retentionMean (micro minutes) for the time dimension

diff -r ecd3f6c9e606 -r b1015b9241cd MsClust.jar
Binary file MsClust.jar has changed
diff -r ecd3f6c9e606 -r b1015b9241cd msclust.xml
--- a/msclust.xml	Thu May 01 11:19:52 2014 +0200
+++ b/msclust.xml	Fri May 09 17:07:58 2014 +0200
@@ -1,4 +1,4 @@
-<tool name="MsClust" id="msclust2" version="2.0.3">
+<tool name="MsClust" id="msclust2" version="2.0.4">
 	<description>Extracts fragmentation spectra from aligned data</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -25,8 +25,9 @@
 		-pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf
 		-pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold
 		-pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
-		-scanDistTol $potDensFuncType.pdf_scan_toler 
-		-scanDistanceConfidence $potDensFuncType.pdf_scan_conf  
+		-rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type
+		-rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler
+		-rtDistanceConfidence $potDensFuncType.pdf_scan_conf  
 		-centrotypesOut $centrotypesOut 
 		-simOut $simOut
 		-micOut $micOut
@@ -91,7 +92,18 @@
 		    </param>
 		    <when value="original">
 		      <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks"  />
-		      <param name="pdf_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
+		      <conditional name="rt_dist_tol_unit">
+		      	<param name="type" type="select" size="30" label="Peak time unit">
+		      		<option value="1" selected="true">scan nr</option>
+		      		<option value="2" selected="true">(average) micro minutes</option>
+		      	</param>
+		      	<when  value="1">
+		      		<param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
+		      	</when>
+		      	<when  value="2">
+		      		<param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
+		      	</when>
+		      </conditional>
 		      <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
 		      <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
 		      <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />