Mercurial > repos > jpayne > bam_dealer
comparison paired_bam_dealer.xml @ 0:6325216db1fe
planemo upload
| author | jpayne |
|---|---|
| date | Wed, 06 Dec 2017 10:26:15 -0500 |
| parents | |
| children | bd0524e92afd |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:6325216db1fe |
|---|---|
| 1 <tool id="paired_bam_dealer" name="Deal out" version="0.1.0"> | |
| 2 <description>paired-end reads by alignment or non-alignment to a reference</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.2">samtools</requirement> | |
| 5 <requirement type="package" version="2.26">bedtools</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam )) | |
| 9 -fq $mapped_1 | |
| 10 -fq2 $mapped_2 && echo "mapped out" && | |
| 11 bamToFastq -i <( | |
| 12 samtools merge -u - | |
| 13 <(samtools view -u -f 4 -F 264 $input_bam) | |
| 14 <(samtools view -u -f 8 -F 260 $input_bam) | |
| 15 <(samtools view -u -f 12 -F 256 $input_bam) | |
| 16 | samtools sort -n | |
| 17 ) | |
| 18 -fq $unmapped_1 | |
| 19 -fq2 $unmapped_2 && echo "unmapped out" | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 22 <param format="bam" name="input_bam" type="data" label="BAM alignment" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="fastqsanger" label="unmapping reads, reverse" name="unmapped_2" /> | |
| 26 <data format="fastqsanger" label="unmapping reads, forward" name="unmapped_1" /> | |
| 27 <data format="fastqsanger" label="mapping reads, reverse" name="mapped_2" /> | |
| 28 <data format="fastqsanger" label="mapping reads, forward" name="mapped_1" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input_bam" value="mapped_reads.bam" /> | |
| 33 <output name="mapped_1" value="forward_mapped.fastq" /> | |
| 34 <output name="mapped_2" value="reverse_mapped.fastq" /> | |
| 35 <output name="unmapped_1" value="forward_unmapped.fastq" /> | |
| 36 <output name="unmapped_2" value="reverse_unmapped.fastq" /> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help><![CDATA[ | |
| 40 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. | |
| 41 ]]></help> | |
| 42 | |
| 43 <citations> | |
| 44 </citations> | |
| 45 </tool> |