<tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0">
	<description> </description>
	<command interpreter="bash">
		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
	</command>
	<inputs>
	<param name="in_file" format="tabular" type="data" label="Data to Process" />
	<param name="clonaltype_select" type="select" label="Clonal Type Definition">
		<option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
		<option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
		<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
		<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
		<option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
	</param>

	<param name="species" type="select" label="Species">
		<option value="human">Human</option>
		<option value="mouse">Mouse</option>
	</param>

	<param name="locus" type="select" label="Locus">
		<option value="trb">TRB</option>
		<option value="tra">TRA</option>
		<option value="trg">TRG</option>
		<option value="trd">TRD</option>
	</param>

	<param name="selection" type="select" label="Selection">
		<option value="unique">Unique (Based on clonaltype)</option>
		<option value="all">All</option>
	</param>
	</inputs>
	<outputs>
		<data format="html" name="out_file" />
	</outputs>
	<help>
		Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
	</help>
</tool>