# HG changeset patch
# User devteam
# Date 1431118289 14400
# Node ID aa0ef6f0ee89ae64f39ce4f45aeebaeef1a65ef1
# Parent  c6fdfe3331d69b741ede3d76bcdd39d92b6fbb64
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6

diff -r c6fdfe3331d6 -r aa0ef6f0ee89 samtools_mpileup.xml
--- a/samtools_mpileup.xml	Tue Apr 21 16:29:10 2015 -0400
+++ b/samtools_mpileup.xml	Fri May 08 16:51:29 2015 -0400
@@ -33,14 +33,14 @@
         #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
             -l "$pasted_regions"
         #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
-            -l "$bed_regions"
+            -l "$advanced_options.limit_by_region.bed_regions"
         #end if
         #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
             -G "$excluded_read_groups"
         #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
-            -G "$read_groups"
+            -G "$advanced_options.exclude_read_group.read_groups"
         #end if
-            ${advanced_options.skip_anomalous_read_pairs}
+        ${advanced_options.skip_anomalous_read_pairs}
         ${advanced_options.disable_probabilistic_realignment}
         -C "${advanced_options.coefficient_for_downgrading}"
         -d "${advanced_options.max_reads_per_bam}"
@@ -241,6 +241,7 @@
                 <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/>
                 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
                 <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/>
+                <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
             </when>
             <when value="basic" />
         </conditional>