# HG changeset patch
# User greg
# Date 1503414382 14400
# Node ID 8d8f796a3bdab9d752f3350b1a0b86e45f68e454
# Parent  695053a23fe4378b57832bf050ec687fe08df4af
Uploaded

diff -r 695053a23fe4 -r 8d8f796a3bda ideas.xml
--- a/ideas.xml	Tue Aug 22 09:54:49 2017 -0400
+++ b/ideas.xml	Tue Aug 22 11:06:22 2017 -0400
@@ -46,9 +46,8 @@
     -bychr
 #end if
 -c $reads_per_bp
-#set blacklist_regions = $blacklist_regions_cond.blacklist_regions
-#if str($blacklist_regions) == 'yes':
-    -exclude '$blacklist_regions_cond.blacklist_input'
+#if str($blacklist_input) not in ['None', '']:
+    -exclude '$blacklist_input'
 #end if
 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets
 #if str($standardize_datasets) == 'yes':
@@ -197,10 +196,10 @@
         <param name="max_position_classes" type="integer" value="0" min="0" label="Maximum number of position classes to be inferred" help="Zero value has no affect"/>
         <param name="max_cell_type_clusters" type="integer" value="0" min="0" label="Maximum number of cell type clusters allowed" help="Zero value has no affect"/>
         <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default value: sqrt(number of cell types)"/>
-        <param name="burnin_num" type="integer" value="50" min="1" label="Number of burnin steps"/>
-        <param name="mcmc_num" type="integer" value="50" min="1" label="Number of maximization steps"/>
+        <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
+        <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
         <param name="min_standard_dev" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 0.5"/>
-        <param name="max_standard_dev" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: infinity"/>
+        <param name="max_standard_dev" type="float" value="0" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: infinity"/>
     </inputs>
     <outputs>
         <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/>