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1 <tool id="BAMTools_bamToFastX" name="convert BAM to FASTA/Q">
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2 <description/>
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3 <requirements>
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4 <requirement type="package" version="2.3.0">bamtools</requirement>
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5 </requirements>
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6 <command>
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7 bamtools convert -in '$input1' -out '$output' -format $format
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8 </command>
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9 <inputs>
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10 <param format="bam" name="input1" type="data" label="BAM file"/>
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11 <param name="format" type="select" label="Output Format">
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12 <option value="fastq">FASTQ</option>
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13 <option value="fasta">FASTA</option>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="fastqsanger" name="output" metadata_source="input1" >
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18 <change_format>
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19 <when input="format" value="fasta" format="fasta"/>
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20 </change_format>
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21 </data>
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22 </outputs>
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23 <help>
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24 **What it does** This tools converts a BAM file to a FASTQ or FASTA file. ------- *bamtools convert* is part of the `BAMTools package`__ by Derek Barnett. .. __: https://github.com/pezmaster31/bamtools ------- This wrapper was originally created by A. Gordon.
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25 </help>
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26 </tool>
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