<tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@">
    <macros>
        <token name="@WRAPPER_VERSION@">332</token>
    </macros>

    <description>Convert all or part of .2bit file to fasta</description>

    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement>
    </requirements>

    <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>

    <command>
<![CDATA[
        twoBitToFa
            '$twobit_input'
            '$fasta_output'

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

            #if $start
              -start=$start
            #end if

            #if $end
              -end=$end
            #end if

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

            $noMask
]]>
    </command>

    <inputs>
        <param name="twobit_input" type="data" format="twobit"
          label="Input TwoBit file" help=""/>

        <param argument="-seq" type="text" label="Restrict this to just one sequence
           (Optional)" help="" optional="True"/>

        <param argument="-start" type="integer" label="Start at given position in
          sequence (Optional)" help="Zero-based" optional="True"/>

        <param argument="-end" type="integer" label="End at given position in
          sequence (Optional)" help="Non-inclusive" optional="True"/>

        <param argument="-seqList" type="data" format="txt"
          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)"
          optional="True"/>

        <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue=""
          checked="false" label="Convert sequence to all upper case?" help=""/>
    </inputs>

    <outputs>
        <data format="fasta" name="fasta_output"/>
    </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/>`_.

    ]]></help>

    <citations>
    </citations>
</tool>