# HG changeset patch
# User iuc
# Date 1532447395 14400
# Node ID 6bb3cd0182030f2ffc43079d0e84b97a53c6bd8f
# Parent  6283d16e40ed718bbe0986363666f3b497139722
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b

diff -r 6283d16e40ed -r 6bb3cd018203 coverageBed.xml
--- a/coverageBed.xml	Sun Jun 24 11:52:38 2018 -0400
+++ b/coverageBed.xml	Tue Jul 24 11:49:55 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.3">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -26,7 +26,7 @@
         #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)
+                -sorted  -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
             #end if
         #else:
             #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
@@ -96,6 +96,17 @@
             <output name="output" file="coverageBed_result1.bed" ftype="bed" />
         </test>
         <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="reduce_or_iterate_selector" value="reduce" />
+            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+        </test>
+        <test>
             <param name="inputA" value="coverageBedA.bed" ftype="bed" />
             <param name="inputB" value="coverageBedB.bed" ftype="bed" />
             <param name="overlap_b" value="1"  />
diff -r 6283d16e40ed -r 6bb3cd018203 test-data/multicov1_by_srma_in3.cov.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multicov1_by_srma_in3.cov.bed	Tue Jul 24 11:49:55 2018 -0400
@@ -0,0 +1,2 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522