view tools/samtools_bam2fq/samtools_bam2fq.xml @ 0:1b9ed562835c draft

Uploaded v0.0.1, handles default behaviour only (SAM/BAM to FASTQ, no options).

<tool id="samtools_bam2fq" name="Convert BAM to FASTQ" version="0.0.1">
    <description>samtools bam2fq</description>
    <requirements>
        <requirement type="binary">samtools</requirement>
        <requirement type="package" version="1.1">samtools</requirement>
    </requirements>
    <version_command>samtools 2&gt;&amp;1 | grep -i "Version:"</version_command>
    <command>samtools bam2fq "$input_bam" &gt; "$out_fastq"</command>
    <inputs>
        <!-- Unlike other bits of samtools, this seems to autodetect SAM vs BAM -->
        <param name="input_bam" type="data" format="bam,sam" label="Input BAM file" />
	<!-- TODO - new options -n, -O and -s in samtools v1.1 -->
    </inputs>
    <outputs>
        <data name="out_fastq" format="fastqsanger" label="$input_bam.name (bam2fq)" />
    </outputs>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <tests>
        <test>
            <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
            <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
            <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_bam" value="sam_spec_padded.depad.bam" ftype="bam" />
            <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
        </test>
    </tests>
    <help>
**What it does**

This tool runs the ``samtools bam2fq`` command in the SAMtools toolkit.

It is quite common to wish to remap high-throughput sequencing data. If you
only have the mapped reads in SAM/BAM format, this tool can "unmap" them to
recover FASTQ format reads to input into an alternative mapping tool.

BAM files can hold both aligned reads and unaligned reads, so another example
usage would be to filter your BAM file to get only the unaligned reads, and
turn those back in FASTQ using this tool ready for *de novo* assembly, or to
try mapping against another reference sequence.


**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite:

Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
Bioinformatics 25(16), 2078-9.
http://dx.doi.org/10.1093/bioinformatics/btp352

Peter J.A. Cock (2014), Galaxy wrapper for the samtools bam2fq command
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp352</citation>
    </citations>
</tool>