--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/paired_bam_dealer.xml	Wed Dec 06 10:26:15 2017 -0500
@@ -0,0 +1,45 @@
+<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="package" version="1.2">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"
+    ]]></command>
+    <inputs>
+    	<param format="bam" name="input_bam" type="data" label="BAM alignment" />
+    </inputs>
+    <outputs>
+    	<data format="fastqsanger" label="unmapping reads, reverse" name="unmapped_2" />
+    	<data format="fastqsanger" label="unmapping reads, forward" name="unmapped_1" />
+    	<data format="fastqsanger" label="mapping reads, reverse" name="mapped_2" />
+    	<data format="fastqsanger" label="mapping reads, forward" name="mapped_1" />
+    </outputs>
+    <tests>
+    	<test>
+    		<param name="input_bam" value="mapped_reads.bam" />
+    		<output name="mapped_1" value="forward_mapped.fastq" />
+    		<output name="mapped_2" value="reverse_mapped.fastq" />
+    		<output name="unmapped_1" value="forward_unmapped.fastq" />
+    		<output name="unmapped_2" value="reverse_unmapped.fastq" />
+    	</test>
+    </tests>
+    <help><![CDATA[
+        Input is a BAM alignment of paired-end reads to a reference. Output is paired-end files of reads mapping and reads not mapping to reference.
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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