<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" 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"
#if $gene_selection.source == "imgtdb"		
	"${gene_selection.species}" "${gene_selection.locus}" $filterproductive ${clonality_method}
#else
	"custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
#end if
	</command>
	<inputs>
		<repeat name="patients" title="Donor" 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 (AA)</option>
			<option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3 (nt)</option>
			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3 (AA)</option>
			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3 (nt)</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 (nt)</option>
		</param>
		
		<conditional name="gene_selection" >
			<param name="source" type="select" label="Order of V(D)J genes in graphs" help="" >
					<option value="imgtdb" selected="true">IMGT-DB</option>
					<option value="custom">User defined</option>
			</param>
			<when value="imgtdb">
				<param name="species" type="select" label="Species">
					<option value="Homo sapiens functional">Homo sapiens functional</option>
					<option value="Homo sapiens">Homo sapiens</option>
					<option value="Homo sapiens non-functional">Homo sapiens non-functional</option>
					<option value="Bos taurus">Bos taurus</option>
					<option value="Bos taurus functional">Bos taurus functional</option>
					<option value="Bos taurus non-functional">Bos taurus non-functional</option>
					<option value="Camelus dromedarius">Camelus dromedarius</option>
					<option value="Camelus dromedarius functional">Camelus dromedarius functional</option>
					<option value="Camelus dromedarius non-functional">Camelus dromedarius non-functional</option>
					<option value="Canis lupus familiaris">Canis lupus familiaris</option>
					<option value="Canis lupus familiaris functional">Canis lupus familiaris functional</option>
					<option value="Canis lupus familiaris non-functional">Canis lupus familiaris non-functional</option>
					<option value="Danio rerio">Danio rerio</option>
					<option value="Danio rerio functional">Danio rerio functional</option>
					<option value="Danio rerio non-functional">Danio rerio non-functional</option>
					<option value="Macaca mulatta">Macaca mulatta</option>
					<option value="Macaca mulatta functional">Macaca mulatta functional</option>
					<option value="Macaca mulatta non-functional">Macaca mulatta non-functional</option>
					<option value="Mus musculus">Mus musculus</option>
					<option value="Mus musculus functional">Mus musculus functional</option>
					<option value="Mus musculus non-functional">Mus musculus non-functional</option>
					<option value="Mus spretus">Mus spretus</option>
					<option value="Mus spretus functional">Mus spretus functional</option>
					<option value="Mus spretus non-functional">Mus spretus non-functional</option>
					<option value="Oncorhynchus mykiss">Oncorhynchus mykiss</option>
					<option value="Oncorhynchus mykiss functional">Oncorhynchus mykiss functional</option>
					<option value="Oncorhynchus mykiss non-functional">Oncorhynchus mykiss non-functional</option>
					<option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
					<option value="Ornithorhynchus anatinus functional">Ornithorhynchus anatinus functional</option>
					<option value="Ornithorhynchus anatinus non-functional">Ornithorhynchus anatinus non-functional</option>
					<option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
					<option value="Oryctolagus cuniculus functional">Oryctolagus cuniculus functional</option>
					<option value="Oryctolagus cuniculus non-functional">Oryctolagus cuniculus non-functional</option>
					<option value="Rattus norvegicus">Rattus norvegicus</option>
					<option value="Rattus norvegicus functional">Rattus norvegicus functional</option>
					<option value="Rattus norvegicus non-functional">Rattus norvegicus non-functional</option>
					<option value="Sus scrofa">Sus scrofa</option>
					<option value="Sus scrofa functional">Sus scrofa functional</option>
					<option value="Sus scrofa non-functional">Sus scrofa non-functional</option>
				</param>
			
				<param name="locus" type="select" label="Locus">
					<option value="TRA">TRA</option>
					<option value="TRD">TRD</option>
					<option value="TRG">TRG</option>
					<option value="TRB">TRB</option>
					<option value="IGH">IGH</option>
					<option value="IGI">IGI</option>
					<option value="IGK">IGK</option>
					<option value="IGL">IGL</option>
				</param>
			</when>
			<when value="custom">
				<param name="species" type="hidden" value="custom" size="50" />
				<param name="vgenes" type="text" label="V Genes, add the custom genes comma seperated, no spaces" size="100" />
				<param name="dgenes" type="text" label="D Genes" size="100" />
				<param name="jgenes" type="text" label="J Genes" size="100" />
			</when>
		</conditional>
		
		<param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs ">
			<option value="yes">Yes</option>
			<option value="no">No</option>
		</param>
		
		<param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package">
			<option value="old">Old</option>
			<option value="boyd">R Package (needs 3 replicate minimum)</option>
		</param>
	</inputs>
	<outputs>
		<data format="html" name="out_file" />
	</outputs>
	<requirements>
		<requirement type="package" version="0.6">igblastwrp</requirement>
		<requirement type="package" version="3.3">weblogo</requirement>
		<!--<requirement type="package" version="0.20">circostools</requirement>-->
	</requirements>
	<help>
		The entire Immune Repertoire pipeline as a single tool, input several FASTA files or IMGT zip/txz files, give them an ID and it will BLAST/parse, merge and plot them.

		.. class:: warningmark

Custom gene ordering based on position on genome: 

**Human**

IGH::

    V:
    IGHV7-81,IGHV3-74,IGHV3-73,IGHV3-72,IGHV3-71,IGHV2-70,IGHV1-69,IGHV3-66,IGHV3-64,IGHV4-61,IGHV4-59,IGHV1-58,IGHV3-53,IGHV3-52,IGHV5-a,IGHV5-51,IGHV3-49,IGHV3-48,IGHV3-47,IGHV1-46,IGHV1-45,IGHV3-43,IGHV4-39,IGHV3-35,IGHV4-34,IGHV3-33,IGHV4-31,IGHV4-30-4,IGHV4-30-2,IGHV3-30-3,IGHV3-30,IGHV4-28,IGHV2-26,IGHV1-24,IGHV3-23,IGHV3-22,IGHV3-21,IGHV3-20,IGHV3-19,IGHV1-18,IGHV3-15,IGHV3-13,IGHV3-11,IGHV3-9,IGHV1-8,IGHV3-7,IGHV2-5,IGHV7-4-1,IGHV4-4,IGHV4-b,IGHV1-3,IGHV1-2,IGHV6-1
    D:
    IGHD1-1,IGHD2-2,IGHD3-3,IGHD6-6,IGHD1-7,IGHD2-8,IGHD3-9,IGHD3-10,IGHD4-11,IGHD5-12,IGHD6-13,IGHD1-14,IGHD2-15,IGHD3-16,IGHD4-17,IGHD5-18,IGHD6-19,IGHD1-20,IGHD2-21,IGHD3-22,IGHD4-23,IGHD5-24,IGHD6-25,IGHD1-26,IGHD7-27
    J:
    IGHJ1,IGHJ2,IGHJ3,IGHJ4,IGHJ5,IGHJ6


IGK::

    V:
    IGKV3D-7,IGKV1D-8,IGKV1D-43,IGKV3D-11,IGKV1D-12,IGKV1D-13,IGKV3D-15,IGKV1D-16,IGKV1D-17,IGKV3D-20,IGKV2D-26,IGKV2D-28,IGKV2D-29,IGKV2D-30,IGKV1D-33,IGKV1D-39,IGKV2D-40,IGKV2-40,IGKV1-39,IGKV1-33,IGKV2-30,IGKV2-29,IGKV2-28,IGKV1-27,IGKV2-24,IGKV3-20,IGKV1-17,IGKV1-16,IGKV3-15,IGKV1-13,IGKV1-12,IGKV3-11,IGKV1-9,IGKV1-8,IGKV1-6,IGKV1-5,IGKV5-2,IGKV4-1
    J:
    IGKJ1,IGKJ2,IGKJ3,IGKJ4,IGKJ5


IGL::

    V:
    IGLV4-69,IGLV8-61,IGLV4-60,IGLV6-57,IGLV5-52,IGLV1-51,IGLV9-49,IGLV1-47,IGLV7-46,IGLV5-45,IGLV1-44,IGLV7-43,IGLV1-41,IGLV1-40,IGLV5-39,IGLV5-37,IGLV1-36,IGLV3-27,IGLV3-25,IGLV2-23,IGLV3-22,IGLV3-21,IGLV3-19,IGLV2-18,IGLV3-16,IGLV2-14,IGLV3-12,IGLV2-11,IGLV3-10,IGLV3-9,IGLV2-8,IGLV4-3,IGLV3-1
    J:
    IGLJ1,IGLJ2,IGLJ3,IGLJ6,IGLJ7


TRB::

    V:
    TRBV2,TRBV3-1,TRBV4-1,TRBV5-1,TRBV6-1,TRBV4-2,TRBV6-2,TRBV4-3,TRBV6-3,TRBV7-2,TRBV6-4,TRBV7-3,TRBV9,TRBV10-1,TRBV11-1,TRBV10-2,TRBV11-2,TRBV6-5,TRBV7-4,TRBV5-4,TRBV6-6,TRBV5-5,TRBV7-6,TRBV5-6,TRBV6-8,TRBV7-7,TRBV6-9,TRBV7-8,TRBV5-8,TRBV7-9,TRBV13,TRBV10-3,TRBV11-3,TRBV12-3,TRBV12-4,TRBV12-5,TRBV14,TRBV15,TRBV16,TRBV18,TRBV19,TRBV20-1,TRBV24-1,TRBV25-1,TRBV27,TRBV28,TRBV29-1,TRBV30
    D:
    TRBD1,TRBD2
    J:
    TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ1-6,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7


TRA::

    V:
    TRAV1-1,TRAV1-2,TRAV2,TRAV3,TRAV4,TRAV5,TRAV6,TRAV7,TRAV8-1,TRAV9-1,TRAV10,TRAV12-1,TRAV8-2,TRAV8-3,TRAV13-1,TRAV12-2,TRAV8-4,TRAV13-2,TRAV14/DV4,TRAV9-2,TRAV12-3,TRAV8-6,TRAV16,TRAV17,TRAV18,TRAV19,TRAV20,TRAV21,TRAV22,TRAV23/DV6,TRAV24,TRAV25,TRAV26-1,TRAV27,TRAV29/DV5,TRAV30,TRAV26-2,TRAV34,TRAV35,TRAV36/DV7,TRAV38-1,TRAV38-2/DV8,TRAV39,TRAV40,TRAV41
    J:
    TRAJ57,TRAJ56,TRAJ54,TRAJ53,TRAJ52,TRAJ50,TRAJ49,TRAJ48,TRAJ47,TRAJ46,TRAJ45,TRAJ44,TRAJ43,TRAJ42,TRAJ41,TRAJ40,TRAJ39,TRAJ38,TRAJ37,TRAJ36,TRAJ34,TRAJ33,TRAJ32,TRAJ31,TRAJ30,TRAJ29,TRAJ28,TRAJ27,TRAJ26,TRAJ24,TRAJ23,TRAJ22,TRAJ21,TRAJ20,TRAJ18,TRAJ17,TRAJ16,TRAJ15,TRAJ14,TRAJ13,TRAJ12,TRAJ11,TRAJ10,TRAJ9,TRAJ8,TRAJ7,TRAJ6,TRAJ5,TRAJ4,TRAJ3


TRG::

    V:
    TRGV9,TRGV8,TRGV5,TRGV4,TRGV3,TRGV2
    J:
    TRGJ2,TRGJP2,TRGJ1,TRGJP1


TRD::

    V:
    TRDV1,TRDV2,TRDV3
    D:
    TRDD1,TRDD2,TRDD3
    J:
    TRDJ1,TRDJ4,TRDJ2,TRDJ3


**Mouse**

TRB::

    V:
    TRBV1,TRBV2,TRBV3,TRBV4,TRBV5,TRBV12-1,TRBV13-1,TRBV12-2,TRBV13-2,TRBV13-3,TRBV14,TRBV15,TRBV16,TRBV17,TRBV19,TRBV20,TRBV23,TRBV24,TRBV26,TRBV29,TRBV30,TRBV31
    D:
    TRBD1,TRBD2
    J:
    TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
    
	</help>

</tool>