# HG changeset patch
# User jpayne
# Date 1512667462 18000
# Node ID 55df0d1c6365ce499fdeddd42f1325a4bc3f2ac9
# Parent  881a24a35480809c16497c74d43eceb01abb98e8
planemo upload commit b'5e9a6cdf7bbe14678aa83ae2304bde4b6ad2976d\n'

diff -r 881a24a35480 -r 55df0d1c6365 paired_bam_dealer.xml
--- a/paired_bam_dealer.xml	Wed Dec 06 16:41:46 2017 -0500
+++ b/paired_bam_dealer.xml	Thu Dec 07 12:24:22 2017 -0500
@@ -5,7 +5,18 @@
     	<requirement type="package" version="2.26">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-		which -a samtools ; ldd `which samtools`
+        bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam  )) 
+        	-fq $mapped_1
+        	-fq2 $mapped_2		&& 	echo "mapped out"	&&
+        bamToFastq -i <(
+        	samtools merge -u -
+        					  <(samtools view -u -f 4  -F 264 $input_bam)
+        					  <(samtools view -u -f 8  -F 260 $input_bam)
+        					  <(samtools view -u -f 12 -F 256 $input_bam)
+        		| samtools sort -n 
+        	)
+        	-fq $unmapped_1
+        	-fq2 $unmapped_2	&& echo "unmapped out"
     ]]></command>
     <inputs>
     	<param format="bam" name="input_bam" type="data" label="BAM alignment" />