# HG changeset patch
# User iuc
# Date 1485171786 18000
# Node ID fadebae7e69bb77b933db20dc09ea674ddec1e6e
# Parent  7b3aaff0d78cafb500ccd03c8f3545b6bf74ecf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377

diff -r 7b3aaff0d78c -r fadebae7e69b intersectBed.xml
--- a/intersectBed.xml	Fri Oct 28 12:54:40 2016 -0400
+++ b/intersectBed.xml	Mon Jan 23 06:43:06 2017 -0500
@@ -11,7 +11,7 @@
         #set modes = ' '.join( str($overlap_mode).split(',') )
 
         bedtools intersect
-            #if $inputA.ext == "bam":
+            #if $inputA.is_of_type('bam'):
                 -abam "${inputA}"
             #else:
                 -a "${inputA}"
diff -r 7b3aaff0d78c -r fadebae7e69b macros.xml
--- a/macros.xml	Fri Oct 28 12:54:40 2016 -0400
+++ b/macros.xml	Mon Jan 23 06:43:06 2017 -0500
@@ -161,7 +161,7 @@
 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
 
 .. _bedtools package: https://github.com/arq5x/bedtools2
-.. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/
+.. _Quinlan laboratory: http://quinlanlab.org
 
 
 **Citation**
diff -r 7b3aaff0d78c -r fadebae7e69b reldist.xml
--- a/reldist.xml	Fri Oct 28 12:54:40 2016 -0400
+++ b/reldist.xml	Mon Jan 23 06:43:06 2017 -0500
@@ -8,10 +8,10 @@
     <command>
 <![CDATA[
         bedtools reldist
-        -a $inputA
-        -b $inputB
+        -a '$inputA'
+        -b '$inputB'
         $detail
-        > "$output"
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r 7b3aaff0d78c -r fadebae7e69b windowBed.xml
--- a/windowBed.xml	Fri Oct 28 12:54:40 2016 -0400
+++ b/windowBed.xml	Mon Jan 23 06:43:06 2017 -0500
@@ -8,7 +8,7 @@
     <command>
 <![CDATA[
         bedtools window
-        #if $inputA.ext == "bam":
+        #if $inputA.is_of_type('bam'):
             -abam '$inputA'
         #else:
             -a '$inputA'