<tool id="edu.tamu.cpt.fasta.seq_trans" name="Fasta Translate" version="19.1.0.0">
    <description>Translate fasta file</description>
    <macros>
        <import>macros.xml</import>
    
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/fasta_translate.py'
@SEQUENCE@

--target '${output.format_select}'

#if str($output.format_select) == "protein":
		--table '$output.table'
		'$output.strip_stops'
		'$output.met'
#end if

> '$default']]></command>
    <inputs>
        <expand macro="input/fasta"/>
        <conditional name="output">
            <param label="Target output" type="select" name="format_select">
                <option value="rna">RNA</option>
                <option value="protein" selected="true">Protein</option>
            </param>
            <when value="rna"/>
            <when value="protein">
                <param label="Translation table to use" name="table" type="select">
                    <option value="1">[1] The Standard Code</option>
                    <option value="2">[2] The Vertebrate Mitochondrial Code</option>
                    <option value="3">[3] The Yeast Mitochondrial Code</option>
                    <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
                    <option value="5">[5] The Invertebrate Mitochondrial Code </option>
                    <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
                    <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
                    <option value="10">[10] The Euplotid Nuclear Code</option>
                    <option value="11" selected="true">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
                    <option value="12">[12] The Alternative Yeast Nuclear Code</option>
                    <option value="13">[13] The Ascidian Mitochondrial Code</option>
                    <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
                    <option value="15">[15] Blepharisma Nuclear Code</option>
                    <option value="16">[16] Chlorophycean Mitochondrial Code</option>
                    <option value="21">[21] Trematode Mitochondrial Code</option>
                    <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
                    <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
                    <option value="24">[24] Pterobranchia Mitochondrial Code</option>
                    <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
                </param>
                <param label="Remove stop characters" name="strip_stops" type="boolean" checked="true" truevalue="--strip_stops" falsevalue=""/>
                <param label="Convert first residue to Met" name="met" type="boolean" checked="false" truevalue="--met" falsevalue=""/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fasta" hidden="false" name="default"/>
    </outputs>
    <tests>
        <test>
            <param name="sequences" value="T7_TranslateIn.fasta"/>
            <param name="format_select" value="protein"/>
            <param name="table" value="11"/>
            <param name="strip_stops" value="--strip_stops"/>
            <output name="default" file="T7_TranslateOut.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Translate DNA sequences from an input FASTA or multi-FASTA file to protein or RNA sequences, as selected. 
]]></help>
    <expand macro="citations"/>
</tool>