comparison bamToFastX.xml @ 0:afa51021226c draft

Uploaded
author geert-vandeweyer
date Tue, 18 Feb 2014 04:18:08 -0500
parents
children 76aff7bca1b2
comparison
equal deleted inserted replaced
-1:000000000000 0:afa51021226c
1 <tool id="BAMTools_bamToFastX" name="convert BAM to FASTA/Q">
2 <description/>
3 <requirements>
4 <requirement type="package" version="2.3.0">bamtools</requirement>
5 </requirements>
6 <command>
7 bamtools convert -in '$input1' -out '$output' -format $format
8 </command>
9 <inputs>
10 <param format="bam" name="input1" type="data" label="BAM file"/>
11 <param name="format" type="select" label="Output Format">
12 <option value="fastq">FASTQ</option>
13 <option value="fasta">FASTA</option>
14 </param>
15 </inputs>
16 <outputs>
17 <data format="fastqsanger" name="output" metadata_source="input1" label="$input1.tag (FASTQ/A)">
18 <change_format>
19 <when input="format" value="fasta" format="fasta"/>
20 </change_format>
21 </data>
22 </outputs>
23 <help>
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.
25 </help>
26 </tool>