# HG changeset patch
# User greg
# Date 1511293171 18000
# Node ID 5e545c9030a0447410a0d7ebe13973ed14cc88b8
# Parent  7a5b618675a63856d15e56ff8fdc556ce89144e8
Uploaded

diff -r 7a5b618675a6 -r 5e545c9030a0 ideas.xml
--- a/ideas.xml	Tue Nov 21 14:39:23 2017 -0500
+++ b/ideas.xml	Tue Nov 21 14:39:31 2017 -0500
@@ -9,6 +9,7 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#set window_positions_by_chrom = "window.inv"
 #set output_pdf_dir = "output_pdf_dir"
 #set output_txt_dir = "output_txt_dir"
 #set tmp_dir = "tmp"
@@ -52,6 +53,17 @@
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
 ##############################################
+## If using a genomic window bed file, then
+## generate a text file that categorizes the
+## window positions by chromosome to enable
+## the IDEAS -inv option.
+##############################################
+#if str($specify_genomic_window) == "yes":
+  && python '$__tool_directory__/create_window_positions_by_chrome.py'
+  --input '$specify_genomic_window_cond.bed_input'
+  --output $window_positions_by_chrom
+#end if
+##############################################
 ## Run IDEAS
 ##############################################
 && ideas
@@ -59,6 +71,7 @@
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
 #if str($specify_genomic_window) == "yes":
     '$specify_genomic_window_cond.bed_input'
+    -inv $window_positions_by_chrom
 #else:
     $tmp_dir/*.bed
 #end if