<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.5">
    <description>samtools depad</description>
    <requirements>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/samtools_depad.py --version
    </version_command>
    <command  detect_errors="aggressive">
python $__tool_directory__/samtools_depad.py '$padded_ref' '$input_bam' '$input_bam.ext' '$output_bam'
    </command>
    <inputs>
        <param name="padded_ref" type="data" format="fasta" label="Padded FASTA file (with gap characters)" />
        <param name="input_bam" type="data" format="sam,bam" label="Input SAM or BAM file (mapped against the padded FASTA)" />
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="$input_bam.name (depad)" />
    </outputs>
    <tests>
        <test>
            <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" />
            <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
            <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" />
        </test>
        <test>
            <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" />
            <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
            <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" />
        </test>
    </tests>
    <help>
**What it does**

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

Input is a *padded* FASTA file (with gaps represented by either ``*`` or ``-``
characters) and a SAM or BAM file mapped against this *padded* FASTA file.

The output is a new BAM file mapped against the *unpadded* FASTA file
created by removing all gap characters from the 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 depad command
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

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_depad
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp352</citation>
    </citations>
</tool>