# HG changeset patch
# User rlegendre
# Date 1406627224 14400
# Node ID 14e96571582eceec65998b21bd2d481efd19f9d6
# Parent  5feff08a06ea259a7fedf3f9ab0c09a1c3f5c2a0
Uploaded

diff -r 5feff08a06ea -r 14e96571582e ving_wrapper.xml
--- a/ving_wrapper.xml	Tue Jul 29 03:15:34 2014 -0400
+++ b/ving_wrapper.xml	Tue Jul 29 05:47:04 2014 -0400
@@ -58,7 +58,7 @@
 	<inputs>
 		<repeat name="series" title="Bam file">
 			<param name="bamfile" format="bam" type="data" label="Bam file"/>
-			<param name="description" format="txt" type="text" label="Name for your data" help="Describes each data with a name. The default is the filename."/>
+			<param name="description" format="txt" type="text" label="Name for your data" help="Describes each data with a name."/>
 	    </repeat>
 	  	<param name="strand" type="select" label="Inversed strand" help="Use this if the library type is fr-first-strand. All your bam files will treated the same way.">
 		    <option value="yes" >yes</option>
@@ -85,11 +85,11 @@
 	      		<param name="annotationColorByStrand" type="boolean" truevalue="--annotation-color-by-strand" falsevalue="" checked="True" label="Annotation color by strand" help="Use this if you want the transcripts are colored by the strand." />
 	    	</when>  
 	  	</conditional>  
-	  	<param name="scaleLog" type="boolean" truevalue="--scale-log" falsevalue="" checked="True" label="Scale log" help="Use this if you want a logarithmic scale." />
-	  	<param name="symetricScale" type="boolean" truevalue="--symetric-scale" falsevalue="" checked="True" label="Symetric scale" help="This option is for a symetric scale with the same maximum and minimum for both strand in the 'classic' and 'lines' visualization." />
-	  	<param name="annotationPlacedByStrand" type="boolean" truevalue="--annotation-placed-by-strand" falsevalue="" checked="True" label="Annotation placed by strand" help="Use this if you want the transcripts placed according to their strand. It takes more place, but it can be more clear." />
-	  	<param name="unstrand" type="boolean" truevalue="--unstranded" falsevalue="" checked="True" label="Unstranded" help="Use this for an non-strand-specific visualization." />
-	  	<param name="smoothLength" format="txt" type="text" value="" label="Integer value for smoothing" />
+	  	<param name="scaleLog" type="boolean" truevalue="--scale-log" falsevalue="" checked="False" label="Scale log" help="Use this if you want a logarithmic scale." />
+	  	<param name="symetricScale" type="boolean" truevalue="--symetric-scale" falsevalue="" checked="False" label="Symetric scale" help="This option is for a symetric scale with the same maximum and minimum for both strand in the 'classic' and 'lines' visualization." />
+	  	<param name="annotationPlacedByStrand" type="boolean" truevalue="--annotation-placed-by-strand" falsevalue="" checked="False" label="Annotation placed by strand" help="Use this if you want the transcripts placed according to their strand. It takes more place, but it can be more clear." />
+	  	<param name="unstrand" type="boolean" truevalue="--unstranded" falsevalue="" checked="False" label="Unstranded" help="Use this for an non-strand-specific visualization." />
+	  	<param name="smoothLength" format="txt" type="text" value="" label="Sets the length of the sliding window smoothing. The default is NA and allows ving to compute an optimal length, according to the length of the asked genomic region. If you don't want any smoothing, set this to zero" />
 	 	<conditional name="visuType">
 	  		<param name="visu" type="select" label="Type of visualization" >
 		    	<option value="classic" selected="True">classic</option>
@@ -111,8 +111,8 @@
 	  		</when>	
 	  		
 	 		<when value="lines">
-	 			<param name="linesColors" format="txt" type="text" value="black" label="Sample colors" help="Sets the colors for the lines visualization. Comma-separated list. You must specify as many colors as bam files." />
-	  			<param name="linesType" format="txt" type="text" value="1" label="Sample type lines" help="Sets the kind of lines for the lines visualization. Comma-separated list. You must specify as many line types as bam files."/> 
+	 			<param name="linesColors" format="txt" type="text" value="" label="Sample colors" help="Sets the colors for the lines visualization. Comma-separated list. You must specify as many colors as bam files." />
+	  			<param name="linesType" format="txt" type="text" value="" label="Sample type lines" help="Sets the kind of lines for the lines visualization. Comma-separated list. You must specify as many line types as bam files."/> 
 	  		</when>
 
 	  	</conditional>