view bamToFastX.xml @ 2:2572b6f85654 draft default tip

added samtools requirement to splitonrg

<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>