Mercurial > repos > geert-vandeweyer > bamtools_wrappers
diff bamToFastX.xml @ 0:afa51021226c draft
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| author | geert-vandeweyer |
|---|---|
| date | Tue, 18 Feb 2014 04:18:08 -0500 |
| parents | |
| children | 76aff7bca1b2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamToFastX.xml Tue Feb 18 04:18:08 2014 -0500 @@ -0,0 +1,26 @@ +<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 $format +</command> +<inputs> +<param format="bam" name="input1" type="data" label="BAM file"/> +<param name="format" type="select" label="Output Format"> +<option value="fastq">FASTQ</option> +<option value="fasta">FASTA</option> +</param> +</inputs> +<outputs> +<data format="fastqsanger" name="output" metadata_source="input1" label="$input1.tag (FASTQ/A)"> +<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>