Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality_igg.xml @ 47:d97e1421aa86 draft

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author davidvanzessen
date Wed, 27 Jan 2016 10:25:43 -0500
parents 4d201d22633d
children 5ba0377b7737
line wrap: on
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--- a/report_clonality_igg.xml	Wed Jan 27 08:39:16 2016 -0500
+++ b/report_clonality_igg.xml	Wed Jan 27 10:25:43 2016 -0500
@@ -2,15 +2,15 @@
 	<description> </description>
 	<command interpreter="bash">
 #if $gene_selection.source == "imgtdb"		
-	report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method
+	report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method $filter_uniques
 #else
-	report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
+	report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method $filter_uniques
 #end if
 	</command>
 	<inputs>
 		<param name="in_file" format="tabular" type="data" label="Data to Process" />
 		<param name="clonaltype" type="select" label="Clonal Type Definition (Needed for clonality calculation)">
-			<option value="none">Dont remove duplicates based on clonaltype</option>
+			<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>
@@ -95,6 +95,11 @@
 			<option value="boyd">R Package</option>
 		</param>
 		
+		<param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
+		</param>
+		
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" />