Mercurial > repos > jpayne > bam_dealer

changeset 4:881a24a35480

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planemo upload commit b'f16e028df365af5bc6b4b441152d278a55e40ffe\n'-dirty
author jpayne
date Wed, 06 Dec 2017 16:41:46 -0500
parents b7bbe08d50df
children 55df0d1c6365
files paired_bam_dealer.xml
diffstat 1 files changed, 3 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/paired_bam_dealer.xml	Wed Dec 06 14:45:13 2017 -0500
+++ b/paired_bam_dealer.xml	Wed Dec 06 16:41:46 2017 -0500
@@ -1,22 +1,11 @@
 <tool id="paired_bam_dealer" name="Deal out" version="0.1.0">
 	<description>paired-end reads by alignment or non-alignment to a reference</description>
     <requirements>
-    	<requirement type="Tool_Shed_Package" version="1.5">samtools</requirement>
-    	<requirement type="Tool_Shed_Package" version="2.26">bedtools</requirement>
+    	<requirement type="package" version="1.5">samtools</requirement>
+    	<requirement type="package" version="2.26">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        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"
+		which -a samtools ; ldd `which samtools`
     ]]></command>
     <inputs>
     	<param format="bam" name="input_bam" type="data" label="BAM alignment" />