<?xml version="1.0"?>
<tool id="fa_to_twobit" name="faToTwoBit" version="1.0">
    <description>Converts a FASTA sequence file into a twoBit file</description>

    <macros>
        <import>ucsc_macros.xml</import>
    </macros>

    <expand macro="requirements_twobit" />

    <command detect_errors="exit_code">
<![CDATA[
    faToTwoBit
        "${fasta_input}" ${no_mask} ${strip_version} "${twobit_output}"
]]>
    </command>
    <inputs>
        <param name="fasta_input" type="data" format="fasta" label="FASTA file" />

        <param name="no_mask" type="boolean" checked="true"
            truevalue="-noMask" falsevalue=""
            label="Ignore lower-case masking in fa file"
            help="-noMask" />

        <param name="strip_version" type="boolean" checked="true"
            truevalue="-stripVersion" falsevalue=""
            label="Strip off version number after '.' for GenBank accessions"
            help="-stripVersion" />
    </inputs>
    <outputs>
        <data name="twobit_output" format="twobit" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
            <output name="twobit_output" file="KB462401.unmasked.2bit" />
        </test>
        <test>
            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
            <param name="no_mask" value="" />
            <output name="twobit_output" file="KB462401.masked.2bit" />
        </test>
        <test>
            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
            <param name="strip_version" value="" />
            <output name="twobit_output" file="KB462401.keepversion.2bit" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

faToTwoBit converts a DNA sequence file in FASTA format into a
`twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.

    ]]></help>

    <expand macro="citations" />
</tool>