jpayne@0: <tool id="paired_bam_dealer" name="Deal out" version="0.1.0">
jpayne@0: 	<description>paired-end reads by alignment or non-alignment to a reference</description>
jpayne@0:     <requirements>
jpayne@1:     	<requirement type="package" version="1.5">samtools</requirement>
jpayne@0:     	<requirement type="package" version="2.26">bedtools</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam  )) 
jpayne@0:         	-fq $mapped_1
jpayne@0:         	-fq2 $mapped_2		&& 	echo "mapped out"	&&
jpayne@0:         bamToFastq -i <(
jpayne@0:         	samtools merge -u -
jpayne@0:         					  <(samtools view -u -f 4  -F 264 $input_bam)
jpayne@0:         					  <(samtools view -u -f 8  -F 260 $input_bam)
jpayne@0:         					  <(samtools view -u -f 12 -F 256 $input_bam)
jpayne@0:         		| samtools sort -n 
jpayne@0:         	)
jpayne@0:         	-fq $unmapped_1
jpayne@0:         	-fq2 $unmapped_2	&& echo "unmapped out"
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:     	<param format="bam" name="input_bam" type="data" label="BAM alignment" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:     	<data format="fastqsanger" label="unmapping reads, reverse" name="unmapped_2" />
jpayne@0:     	<data format="fastqsanger" label="unmapping reads, forward" name="unmapped_1" />
jpayne@0:     	<data format="fastqsanger" label="mapping reads, reverse" name="mapped_2" />
jpayne@0:     	<data format="fastqsanger" label="mapping reads, forward" name="mapped_1" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:     	<test>
jpayne@0:     		<param name="input_bam" value="mapped_reads.bam" />
jpayne@0:     		<output name="mapped_1" value="forward_mapped.fastq" />
jpayne@0:     		<output name="mapped_2" value="reverse_mapped.fastq" />
jpayne@0:     		<output name="unmapped_1" value="forward_unmapped.fastq" />
jpayne@0:     		<output name="unmapped_2" value="reverse_unmapped.fastq" />
jpayne@0:     	</test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         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.
jpayne@0:     ]]></help>
jpayne@0: 
jpayne@0:     <citations>
jpayne@0:     </citations>
jpayne@0: </tool>