Mercurial > repos > geert-vandeweyer > bamtools_wrappers
view bamToFastX.xml @ 1:76aff7bca1b2 draft
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author | geert-vandeweyer |
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date | Tue, 18 Feb 2014 05:06:20 -0500 |
parents | afa51021226c |
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<tool id="BAMTools_bamToFastX" name="convert BAM to FASTA/Q"> <description/> <requirements> <requirement type="package" version="2.3.0">bamtools</requirement> </requirements> <command> bamtools convert -in '$input1' -out '$output' -format $format </command> <inputs> <param format="bam" name="input1" type="data" label="BAM file"/> <param name="format" type="select" label="Output Format"> <option value="fastq">FASTQ</option> <option value="fasta">FASTA</option> </param> </inputs> <outputs> <data format="fastqsanger" name="output" metadata_source="input1" > <change_format> <when input="format" value="fasta" format="fasta"/> </change_format> </data> </outputs> <help> **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. </help> </tool>