<tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
    <description>converter</description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output'
]]>
    </command>
    <inputs>
        <param format="fasta" name="input" type="data" label="Library to convert" />

        <param name="mode" type="select" label="Convert">
            <option value="d">RNA to DNA (U to T)</option>
            <option value="r">DNA to RNA (T to U)</option>
        </param>
    </inputs>
    <outputs>
        <data format_source="input" name="output" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fasta_nuc_changer1.fasta" />
            <param name="mode" value="r" />
            <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
        </test>
        <test>
            <param name="input" value="fasta_nuc_changer2.fasta" />
            <param name="mode" value="d" />
            <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
        </test>
    </tests>
    <help>
**What it does**

This tool converts RNA FASTA files to DNA (and vice-versa).

In **RNA-to-DNA** mode, U's are changed into T's.

In **DNA-to-RNA** mode, T's are changed into U's.

--------

**Example**

Input RNA FASTA file ( from Sanger's mirBase )::

    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
    UGAGGUAGUAGGUUGUAUAGUU
    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
    UCCCUGAGACCUCAAGUGUGA
    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
    UGGAAUGUAAAGAAGUAUGUA

Output DNA FASTA file (with RNA-to-DNA mode)::

    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
    TGAGGTAGTAGGTTGTATAGTT
    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
    TCCCTGAGACCTCAAGTGTGA
    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
    TGGAATGTAAAGAAGTATGTA


------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
</tool>