# HG changeset patch
# User greg
# Date 1503577358 14400
# Node ID 6dece3e06a10a4ee1d57d5bd1729329a5e6f18cd
# Parent  4afd642aa3ce64d1e7ef4bd65ec8b7a95cc5bd9b
Uploaded

diff -r 4afd642aa3ce -r 6dece3e06a10 ideas.xml
--- a/ideas.xml	Thu Aug 24 08:18:38 2017 -0400
+++ b/ideas.xml	Thu Aug 24 08:22:38 2017 -0400
@@ -10,6 +10,7 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set tmp_dir = "tmp"
+#set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = "prep_output_config.txt"
 ##############################################
 ## Create the config file and prepare the data
@@ -20,9 +21,9 @@
     #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-    cp '$gen_prep_input_config' "prep_input_config.txt" &&
+    cp '$gen_prep_input_config' $prep_input_config &&
     prepMat
-    '$prep_input_config'
+    $prep_input_config
     #if str($specify_genomic_window) == 'yes':
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
@@ -109,7 +110,7 @@
 && mv ./*.state $output_state
     ]]></command>
     <configfiles>
-        <configfile name="prep_input_config"><![CDATA[
+        <configfile name="gen_prep_input_config"><![CDATA[
 #if $input_type_cond == "datasets" and $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
     #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}