diff report_clonality_igg.xml @ 27:f919965e8816 draft

Uploaded

--- a/report_clonality_igg.xml	Mon Feb 09 08:53:30 2015 -0500
+++ b/report_clonality_igg.xml	Fri Mar 06 09:59:53 2015 -0500
@@ -2,14 +2,14 @@
 	<description> </description>
 	<command interpreter="bash">
 #if $gene_selection.source == "imgtdb"		
-	r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive
+	r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method
 #else
-	r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive
+	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
 #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">
+		<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="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>
@@ -89,6 +89,12 @@
 			<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</option>
+		</param>
+		
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" />