Mercurial > repos > jpayne > bam_dealer

changeset 5:55df0d1c6365

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planemo upload commit b'5e9a6cdf7bbe14678aa83ae2304bde4b6ad2976d\n'
author jpayne
date Thu, 07 Dec 2017 12:24:22 -0500
parents 881a24a35480
children add58a8a67f0
files paired_bam_dealer.xml
diffstat 1 files changed, 12 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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" />