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changeset 40:58451dcd076d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f
author iuc
date Sun, 18 Feb 2018 15:06:49 -0500
parents da6d7bc0a8b0
children c96688f1746d
files coverageBed.xml
diffstat 1 files changed, 9 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/coverageBed.xml	Fri Feb 09 08:59:46 2018 -0500
+++ b/coverageBed.xml	Sun Feb 18 15:06:49 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>