bamToFastq.xml

<tool id="bedtools_bamtofastq" name="BAM to FASTQ" version="2.18.2.0">
    <description>converter</description>
    <requirements>
        <requirement type="package" version="2.18.2">bedtools2</requirement>
    </requirements>
    <version_command>bedtools --version</version_command>
    <command>
        bamToFastq
        #if str($tags):
          -tags      $tags
        #end if
        -i '$input' -fq '$output' 
    </command>
    <inputs>
    	<param format="bam" name="input" type="data" label="Source file"/>
        <param name="tags" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
    </inputs>

    <outputs>
        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
    </outputs>
    <help>

**What it does**

This tool converts a BAM file to a FASTQ file.

.. class:: infomark

By default, each alignment in the BAM file is converted to a FASTQ record in the output file. The order of the records in the resulting FASTQ exactly follows the order of the records in the BAM input file.

.. class:: warningmark

If using a custom BAM alignment TAG as  the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).

.. class:: warningmark

If your BAM alignments are from paired-end sequence data, one can use two outputs to create two distinct FASTQ output files — one for end 1 and one for end 2.

When using this option, it is required that the BAM file is sorted/grouped by the read name. This keeps the resulting records in the two output FASTQ files in the same order. 

------

This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__

    .. __: http://code.google.com/p/bedtools/
    .. __: http://cphg.virginia.edu/quinlan/
    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short

    </help>
</tool>