# HG changeset patch
# User greg
# Date 1502385195 14400
# Node ID 6f486284731d77c683434b9c367ff77d18e54101
# Parent  694d13d8b473931902666fd7f60794a20d26d380
Uploaded

diff -r 694d13d8b473 -r 6f486284731d ideas.xml
--- a/ideas.xml	Thu Aug 10 12:58:33 2017 -0400
+++ b/ideas.xml	Thu Aug 10 13:13:15 2017 -0400
@@ -9,13 +9,8 @@
     </requirements>
     <command><![CDATA[
 #import os
-#set tmp_dir = 'tmp'
-#set prep_output_dir = 'prep_output'
-mkdir -p $tmp_dir &&
-mkdir -p $prep_output_dir &&
-echo "#############################################" &&
-echo $tmp_dir &&
-echo $output_dir &&
+mkdir -p tmp &&
+mkdir -p prep_output &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -59,16 +54,16 @@
 ## Build the R matrix from the prepMat output
 ##############################################
 #set r_matrix_input = None
-#for f in $os.listdir($tmp_dir):
+#for f in $os.listdir('tmp'):
     #if f.endswith('.bed.gz'):
-        #set r_matrix_input = $os.path.join($tmp_dir, $f)
+        #set r_matrix_input = $os.path.join('tmp', $f)
     #end if
 #end for
 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
 && Rscript '$__tool_directory__/build_matrix.R'
 -i $r_matrix_input
 -o '%s.input' % $f
--w $tmp_dir
+-w 'tmp'
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################
@@ -124,10 +119,10 @@
     -maxerr $set_max_standard_dev_cond.max_standard_dev
 #end if
 -thread \${GALAXY_SLOTS:-4}
--o $prep_output_dir
-&& mv $prep_output_dir/*.state $output_state
-&& mv $prep_output_dir/*.para $output_para
-&& mv $prep_output_dir/*cluster $output_cluster
+-o 'prep_output'
+&& mv prep_output/*.state $output_state
+&& mv prep_output/*.para $output_para
+&& mv prep_output/*cluster $output_cluster
     ]]></command>
     <configfiles>
         <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: