Mercurial > repos > iuc > bedtools

changeset 13:fadebae7e69b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
author iuc
date Mon, 23 Jan 2017 06:43:06 -0500
parents 7b3aaff0d78c
children 304a594a7ef6
files intersectBed.xml macros.xml reldist.xml windowBed.xml
diffstat 4 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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}"
--- 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**
--- 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>
--- 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'