Mercurial > repos > pieterlukasse > prims_metabolomics

diff msclust.xml @ 49:f772a5caa86a

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Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents 26b93438f30e
children
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line diff
--- a/msclust.xml	Wed Nov 19 15:11:45 2014 +0100
+++ b/msclust.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -1,4 +1,4 @@
-<tool name="MsClust" id="msclust2" version="2.0.6">
+<tool name="MsClust" id="msclust2" version="2.0.7">
 	<description>Extracts fragmentation spectra from aligned data</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -15,7 +15,7 @@
         #if $imputationMethod.type == "valueRange"
         	-rangeUpperLimit $imputationMethod.rangeUpperLimit
         #end if
-		-plInputFormat "metalign" 
+		-plInputFormat $plInputFormat 
 		-potDensFuncType $potDensFuncType.type 
 		-centerSelectionType $centerSelectionType.type 
 		-clusteringType $clusteringType.type 
@@ -68,11 +68,15 @@
 	</command>
 	<inputs>
 
-	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />
+	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign or XCMS/metaMS output data)" />
+	 	<param name="plInputFormat" type="select" size="30" label="Data format">
+			<option value="metalign"  selected="true">MetAlign</option>
+			<option value="xcms">XCMS/metaMS (beta)</option>
+		</param>
 		<param name="dataType" type="select" size="30" label="Data type">
-				<option value="gcms"  selected="true">GC-MS</option>
-				<option value="lcms">LC-MS</option>
-			</param>
+			<option value="gcms"  selected="true">GC-MS</option>
+			<option value="lcms">LC-MS</option>
+		</param>
 	 	<conditional name="imputationMethod">
 			<param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">
 				<option value="none" >none</option>
@@ -95,8 +99,9 @@
 		      <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks"  />
 		      <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" >(average) micro minutes</option>
+		      		<option value="1" selected="true">scan nr (MetAlign)</option>
+		      		<option value="2" >(average) micro minutes (MetAlign)</option>
+		      		<option value="3" >(average) minutes (XCMS)</option>
 		      	</param>
 		      	<when value="1">
 		      		<param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
@@ -104,6 +109,9 @@
 		      	<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>
+		      	<when value="3">
+		      		<param name="pdf_rt_toler" type="float" size="10" value="0.1" label="Peak Width, in minutes" help="e.g. 0.1=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)" />