view plotting_merged.xml @ 15:c6d0ee9b3d91 draft

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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" $species $locus $filterproductive
	</command>
	<inputs>
		<param name="in_file" format="tabular" type="data" label="Data to Process" />
		<param name="clonaltype" type="select" label="Clonal Type Definition">
			<option value="none">Dont 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>
**INPUT**

One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool

**OUTPUT**

It generates the following result:
	</help>
</tool>