Mercurial > repos > davidvanzessen > report_clonality_igg

diff plotting_merged.xml @ 10:06777331fbd8 draft

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author davidvanzessen
date Thu, 15 May 2014 09:27:22 -0400
parents 08aa67564858
children 866d22e60e60
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line diff
--- a/plotting_merged.xml	Wed Mar 26 11:55:13 2014 -0400
+++ b/plotting_merged.xml	Thu May 15 09:27:22 2014 -0400
@@ -1,17 +1,33 @@
 <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"
+		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="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>