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diff flexbar.xml @ 20:83e3813084f2

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Adjustment of when tags.
author jtilman
date Tue, 21 May 2013 16:01:38 +0200
parents 621fa3daa2a1
children d62311a7bac6
line wrap: on
line diff
--- a/flexbar.xml	Mon Mar 18 18:18:28 2013 +0100
+++ b/flexbar.xml	Tue May 21 16:01:38 2013 +0200
@@ -150,6 +150,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="on">
 				<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
 			</when>
@@ -163,6 +165,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="on">
 				<param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
 				<param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
@@ -174,6 +178,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="on">
 				<param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
 			</when>
@@ -185,6 +191,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="on">
 				<param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
 				<conditional name="cbReads">
@@ -214,6 +222,8 @@
 						<option value="no" selected="true">No</option>
 						<option value="yes">Yes</option>
 					</param>
+					<when value="no">
+					</when>
 					<when value="yes">
 						<param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
 					</when>
@@ -224,6 +234,8 @@
 						<option value="no" selected="true">No</option>
 						<option value="yes">Yes</option>
 					</param>
+					<when value="no">
+					</when>
 					<when value="yes">
 						<param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
 					</when>
@@ -236,6 +248,8 @@
 						<option value="no" selected="true">No</option>
 						<option value="yes">Yes</option>
 					</param>
+					<when value="no">
+					</when>
 					<when value="yes">
 						<param name="bMatch"    size="3" type="integer" value="1"  label="Match" optional="false"/>
 						<param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
@@ -252,6 +266,8 @@
 				<option value="on">On</option>
 			</param>
 			
+			<when value="off">
+			</when>
 			<when value="on">
 				<conditional name="ccAdapters">
 					<param name="select" type="select" label="Adapter source">
@@ -283,6 +299,8 @@
 						<option value="no" selected="true">No</option>
 						<option value="yes">Yes</option>
 					</param>
+					<when value="no">
+					</when>
 					<when value="yes">
 						<param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
 					</when>
@@ -296,6 +314,8 @@
 						<option value="no" selected="true">No</option>
 						<option value="yes">Yes</option>
 					</param>
+					<when value="no">
+					</when>
 					<when value="yes">
 						<param name="aMatch"    size="3" type="integer" value="1"  label="Match" optional="false"/>
 						<param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
@@ -311,6 +331,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="on">
 				<param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
 			</when>
@@ -324,6 +346,8 @@
 				<option value="off" selected="true">Off</option>
 				<option value="show">Show</option>
 			</param>
+			<when value="off">
+			</when>
 			<when value="show">
 				<param name="logLevel" type="select" label="Alignment logging">
 					<option value="" selected="true">Off</option>