# HG changeset patch
# User greg
# Date 1503515020 14400
# Node ID ec0e85a08def4f7fdb1cfcdd887764955256c5e5
# Parent  9fbd77da30438fc5377c7ac6073135712a53e8ec
Uploaded

diff -r 9fbd77da3043 -r ec0e85a08def ideas.xml
--- a/ideas.xml	Wed Aug 23 14:58:43 2017 -0400
+++ b/ideas.xml	Wed Aug 23 15:03:40 2017 -0400
@@ -9,12 +9,9 @@
         <requirement type="package" version="1.3.2">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#import os
 #set tmp_dir = 'tmp'
+#set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = 'prep_output_config.txt'
-##set ideas_input_dir = 'ideas_input'
-##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
-##mkdir -p $ideas_input_dir &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -23,14 +20,14 @@
     #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':
-        cp '$extract_prep_input_config' "prep_input_config.txt" &&
+        cp '$extract_prep_input_config' $prep_input_config &&
     #else:
-        cp '$manual_prep_input_config' "prep_input_config.txt" &&
+        cp '$manual_prep_input_config' $prep_input_config &&
     #end if
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     prepMat
-    "prep_input_config.txt"
+    $prep_input_config
     #if str($specify_genomic_window) == 'yes':
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
@@ -57,7 +54,7 @@
 ## Coerce the prepMat config output to the
 ## format expected by the R matrix builder.
 ##############################################
-&& cut -d' ' prep_input_config.txt -f1,2 > file1.txt
+&& cut -d' ' $prep_input_config -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################