annotate paired_bam_dealer.xml @ 4:881a24a35480
planemo upload commit b'f16e028df365af5bc6b4b441152d278a55e40ffe\n'-dirty
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jpayne |
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Wed, 06 Dec 2017 16:41:46 -0500 |
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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="1.5">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 which -a samtools ; ldd `which samtools`
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9 ]]></command>
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10 <inputs>
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11 <param format="bam" name="input_bam" type="data" label="BAM alignment" />
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12 </inputs>
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13 <outputs>
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14 <data format="fastqsanger" label="unmapping reads, reverse" name="unmapped_2" />
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15 <data format="fastqsanger" label="unmapping reads, forward" name="unmapped_1" />
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16 <data format="fastqsanger" label="mapping reads, reverse" name="mapped_2" />
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17 <data format="fastqsanger" label="mapping reads, forward" name="mapped_1" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input_bam" value="mapped_reads.bam" />
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22 <output name="mapped_1" value="forward_mapped.fastq" />
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23 <output name="mapped_2" value="reverse_mapped.fastq" />
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24 <output name="unmapped_1" value="forward_unmapped.fastq" />
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25 <output name="unmapped_2" value="reverse_unmapped.fastq" />
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 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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30 ]]></help>
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31
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32 <citations>
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33 </citations>
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34 </tool> |
