Mercurial > repos > ulfschaefer > phephenix

changeset 12:e252b0b9dd99 draft

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Uploaded
author ulfschaefer
date Thu, 16 Jun 2016 10:44:40 -0400
parents a3f15f50a4af
children b26e4f861e08
files filter_vcf.xml
diffstat 1 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/filter_vcf.xml	Thu Jun 16 08:26:49 2016 -0400
+++ b/filter_vcf.xml	Thu Jun 16 10:44:40 2016 -0400
@@ -53,31 +53,31 @@
 				<option value="mq0f_ratio_option">MQ0F ratio</option>
             </param>
 			<when value="gq_score_option">
-				<param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/>
+				<param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer."/>
 			</when>
 			<when value="dp4_ratio_option">
-				<param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/>
+				<param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float. Only samtools mpileup before version 1.3."/>
 			</when>
 			<when value="ad_ratio_option">
-				<param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/>
+				<param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float. GATK only and samtools from version 1.3."/>
 			</when>
 			<when value="mq_score_option">
-				<param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/>
+				<param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer."/>
 			</when>
 			<when value="min_depth_option">
-				<param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/>
+				<param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer."/>
 			</when>
 			<when value="uncall_gt_option">
 				<param name="uncall_gt" type="text" value="" hidden="True"/>
 			</when>
 			<when value="mq0_ratio_option">
-				<param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/>
+				<param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float. GATK only."/>
 			</when>
 			<when value="qual_score_option">
-				<param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/>
+				<param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer."/>
 			</when>
 			<when value="mq0f_ratio_option">
-				<param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/>
+				<param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float. Samtools only."/>
 			</when>
 		</conditional>
     </repeat>