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