<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>
		<import>cpt-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>