# HG changeset patch
# User iuc
# Date 1518984428 18000
# Node ID 33c3ddea63c5f4ab7ae8e04366cba519ca824996
# Parent  13400f3c3ec54c3564e1bc611817fb8c3d462800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f

diff -r 13400f3c3ec5 -r 33c3ddea63c5 coverageBed.xml
--- a/coverageBed.xml	Fri Feb 09 09:00:06 2018 -0500
+++ b/coverageBed.xml	Sun Feb 18 15:07:08 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -23,11 +23,18 @@
         -a '$inputA'
         #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
             -b '$reduce_or_iterate.inputB'
+            #if $reduce_or_iterate.inputB.is_of_type('bam'):
+                -sorted  -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
+            #end if
         #else:
             #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
             -b '$inputBs'
         #end if
-        | sort -k1,1 -k2,2n
+        #if $inputA.is_of_type('gff') or $inputA.is_of_type('gff3'):
+            | sort -k1,1 -k4,2n
+        #else:
+            | sort -k1,1 -k2,2n
+        #end if
         > '$output'
 ]]>
     </command>