<tool id="ucsc-twobittofa" name="twoBitToFa" version="@TOOL_VERSION@" profile="22.05">
    <description>Convert all or part of .2bit file to FASTA</description>
    <macros>
        <token name="@TOOL_VERSION@">472</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-twobittofa</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command><![CDATA[
twoBitToFa
'$twobit_input'
'$fasta_output'

#if $seq
    -seq='$seq'
#end if

#if str($start)
    -start=$start
#end if

#if str($end)
    -end=$end
#end if

#if $seqList
    -seqList='$seqList'
#end if

$noMask
    ]]></command>

    <inputs>
        <param name="twobit_input" type="data" format="twobit" label="Input TwoBit file" />
        <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" />
        <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/>
        <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" />
        <param argument="-seqList" type="data" format="txt" optional="true"
          label="File containing list of the desired sequence names (Optional)"
          help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
          where coordinates are half-open zero-based, i.e. [start,end)" />
        <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" />
    </inputs>
    <outputs>
        <data name="fasta_output" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="twobit_input" value="input.2bit"/>
            <output name="fasta_output" file="output.fasta" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`twoBitToFa`_ is a tool to convert all or part of .2bit file to FASTA.

For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.

For implementation details see twoBitToFa's `source code`_.

.. _twoBitToFa: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/twoBitToFa/twoBitToFa.c
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>