--- a/blockclust.xml	Mon Jul 21 09:19:13 2014 -0400
+++ b/blockclust.xml	Sun Sep 21 20:41:10 2014 -0400
@@ -42,16 +42,18 @@
                 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
                 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
             #end if
-            BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
+            BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config
             -t $tool_mode.input_bbo
             -a #echo ''.join( $accept_bed )
             -r #echo ''.join( $reject_bed )
             -o $outputdir
+            #if $tool_mode.nochr:
+                -nochr
+            #end if          
             #if str($tool_mode.pred.enable_pred) == "yes":
                 -p
                 -pm $tool_mode.pred.pred_mode
-                -md \$BLOCKCLUST_DATA_PATH/models
-                -x 3;
+                -md \$BLOCKCLUST_DATA_PATH/models;
                 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
                     cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
                 #elif str($tool_mode.pred.pred_mode) == "model_based":
@@ -90,6 +92,7 @@
                     <option value="celWS235">C. elegans (celWS235)</option>
                     <option value="tair10">Arabidopsis thaliana (tair10)</option>
                 </param>
+                <param name="nochr" type="boolean" label="My input files have no 'chr' for chromosome names" checked="False"/>
                 <conditional name="pred">
                     <param name="enable_pred" type="select" label="Would you like to perform classification?">
                         <option value="no">No</option>