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author davidvanzessen
date Thu, 15 May 2014 09:27:22 -0400
parents 08aa67564858
children 866d22e60e60
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<tool id="report_clonality_igg" name="Report Clonality" 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="igh">IGH</option>
			<option value="igk">IGK</option>
			<option value="igl">IGL</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>