<tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0">
	<description> </description>
	<command interpreter="bash">
		complete.sh "
		#for $i, $f in enumerate($patients)
 ${f.id}
            #for $j, $g in enumerate($f.samples)
 ${g.sample}
            #end for
		#end for
" $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
	</command>
	<inputs>
		<repeat name="patients" title="Patients" min="1" default="1">
			<repeat name="samples" title="Sample" min="1" default="1">
					<param name="sample" type="data" label="Sample to Process" />
			</repeat>
			<param name="id" type="text" label="ID" />
		</repeat>
		<param name="clonaltype" type="select" label="Clonal Type Definition">
			<option value="none">Don't remove duplicates based on clonaltype</option>
			<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="igh">IGH</option>
			<option value="igk">IGK</option>
			<option value="igl">IGL</option>
			<option value="trb">TRB</option>
			<option value="tra">TRA</option>
			<option value="trg">TRG</option>
			<option value="trd">TRD</option>
		</param>
		
		<param name="filterproductive" type="select" label="Filter out the unproductive sequences">
			<option value="yes">Yes</option>
			<option value="no">No</option>
		</param>
	</inputs>
	<outputs>
		<data format="html" name="out_file" />
	</outputs>
	<help>
		The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
	</help>
</tool>