Mercurial > repos > greg > ideas

changeset 72:6dece3e06a10 draft

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Uploaded
author greg
date Thu, 24 Aug 2017 08:22:38 -0400
parents 4afd642aa3ce
children 11fe683a0a93
files ideas.xml
diffstat 1 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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}