--- a/ideas.xml	Wed Aug 23 15:03:40 2017 -0400
+++ b/ideas.xml	Wed Aug 23 15:11:44 2017 -0400
@@ -9,17 +9,17 @@
         <requirement type="package" version="1.3.2">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set tmp_dir = 'tmp'
+#set tmp_dir = "tmp"
 #set prep_input_config = "prep_input_config.txt"
-#set prep_output_config = 'prep_output_config.txt'
+#set prep_output_config = "prep_output_config.txt"
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
 #set input_type = $input_type_cond.input_type
-#if str($input_type) == 'datasets':
+#if str($input_type) == "datasets":
     #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
     #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
-    #if str($cell_type_epigenetic_factor) == 'extract':
+    #if str($cell_type_epigenetic_factor) == "extract":
         cp '$extract_prep_input_config' $prep_input_config &&
     #else:
         cp '$manual_prep_input_config' $prep_input_config &&
@@ -28,13 +28,13 @@
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     prepMat
     $prep_input_config
-    #if str($specify_genomic_window) == 'yes':
+    #if str($specify_genomic_window) == "yes":
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
         -gsz '$chromInfo'
         -wsz $specify_genomic_window_cond.window_size
         #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
-        #if str($restrict_chromosomes) == 'yes':
+        #if str($restrict_chromosomes) == "yes":
             #set chroms = []
             #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
             #for $i in $chrom_repeat.chrom
@@ -46,7 +46,7 @@
 #end if
 $bychr
 -c $reads_per_bp
-#if str($blacklist_input) not in ['None', '']:
+#if str($blacklist_input) not in ["None", ""]:
     -exclude '$blacklist_input'
 #end if
 $norm
@@ -69,10 +69,10 @@
 ##############################################
 && ideas
 '$prep_output_config'
-#if str($input_type) == 'datasets':
+#if str($input_type) == "datasets":
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-    #if str($specify_genomic_window) == 'yes':
+    #if str($specify_genomic_window) == "yes":
         '$specify_genomic_window_cond.bed_input'
     #else:
         $tmp_dir/*.bed
@@ -81,29 +81,29 @@
     $tmp_dir/*.bed
 #end if
 $hp
-#if str($log2) != '0.0':
+#if str($log2) != "0.0":
     -log2 $log2
 #end if
-#if str($max_states) != '0.0':
+#if str($max_states) != "0.0":
     -G $max_states
 #end if
-#if str($initial_states) != '0':
+#if str($initial_states) != "0":
     -C $initial_states
 #end if
-#if str($max_position_classes) != '0':
+#if str($max_position_classes) != "0":
     -P $max_position_classes
 #end if
-#if str($max_cell_type_clusters) != '0':
+#if str($max_cell_type_clusters) != "0":
     -K $max_cell_type_clusters
 #end if
-#if str($prior_concentration) != '0.0':
+#if str($prior_concentration) != "0.0":
     -A $prior_concentration
 #end if
 -sample $burnin_num $mcmc_num
-#if str($minerr) != '0.0':
+#if str($minerr) != "0.0":
     -minerr $minerr
 #end if
-#if str($maxerr) != '0.0':
+#if str($maxerr) != "0.0":
     -maxerr $maxerr
 #end if
 -thread \${GALAXY_SLOTS:-4}
@@ -127,13 +127,13 @@
     #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
     #for $i in $cell_type_epigenetic_factor_cond.input:
         #set $file_name_with_ext = $os.path.basename($i)
-        #set $file_name = $file_name_with_ext.split('.')[0]
+        #set $file_name = $file_name_with_ext.split(".")[0]
         #if $input_name_positions == "cell_first":
-            #set $cell_type_name = $file_name.split('-')[0]
-            #set $epigenetic_factor_name = $file_name.split('-')[1]
+            #set $cell_type_name = $file_name.split("-")[0]
+            #set $epigenetic_factor_name = $file_name.split("-")[1]
         #else:
-            #set $cell_type_name = $file_name.split('-')[1]
-            #set $epigenetic_factor_name = $file_name.split('-')[0]
+            #set $cell_type_name = $file_name.split("-")[1]
+            #set $epigenetic_factor_name = $file_name.split("-")[0]
         #end if
 ${cell_type_name} ${epigenetic_factor_name} ${i}
     #end for