Mercurial > repos > rlegendre > ving

changeset 2:14e96571582e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rlegendre
date Tue, 29 Jul 2014 05:47:04 -0400
parents 5feff08a06ea
children d1993299c96e
files ving_wrapper.xml
diffstat 1 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- 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>