# HG changeset patch
# User iuc
# Date 1485171772 18000
# Node ID f0aca67fdb7121e11c683294d6b44e0c559223fb
# Parent  a39035fe518075075bb3b2c50a7f3cd0e8951264
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377

diff -r a39035fe5180 -r f0aca67fdb71 intersectBed.xml
--- a/intersectBed.xml	Fri Oct 28 12:54:27 2016 -0400
+++ b/intersectBed.xml	Mon Jan 23 06:42:52 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 a39035fe5180 -r f0aca67fdb71 macros.xml
--- a/macros.xml	Fri Oct 28 12:54:27 2016 -0400
+++ b/macros.xml	Mon Jan 23 06:42:52 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 a39035fe5180 -r f0aca67fdb71 reldist.xml
--- a/reldist.xml	Fri Oct 28 12:54:27 2016 -0400
+++ b/reldist.xml	Mon Jan 23 06:42:52 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 a39035fe5180 -r f0aca67fdb71 windowBed.xml
--- a/windowBed.xml	Fri Oct 28 12:54:27 2016 -0400
+++ b/windowBed.xml	Mon Jan 23 06:42:52 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'