--- a/ideas.xml	Thu Jan 25 09:48:20 2018 -0500
+++ b/ideas.xml	Thu Jan 25 11:53:07 2018 -0500
@@ -10,6 +10,15 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+## Sylink all files from input.metadata.tmp
+## to the current working directory.
+#import os
+#set tmp_dir = "tmp"
+#set from_tmp_path = $os.path.join($input.extra_files_path, "tmp")
+mkdir $tmp_dir &&
+#for f in $os.listdir($from_tmp_path):
+    ln -s $os.path.join($from_tmp_path, $f) $tmp_dir &&
+#end for
 #set output_pdf_dir = "output_pdf_dir"
 #set output_txt_dir = "output_txt_dir"
 #set output_training_dir = "output_training_dir"
@@ -25,13 +34,13 @@
     #set output_dir = $output_txt_dir
     mkdir '$output_txt_dir' &&
 #end if
-&& Rscript '$__tool_directory__/ideas.R'
+Rscript '$__tool_directory__/ideas.R'
 --burnin_num $burnin_num
 #if str($bychr) == "true":
     --bychr true
 #end if
---chrom_bed_input $input.metadata.chrom_bed_input
---chromosome_windows $input.metadata.chromosome_windows
+--chrom_bed_input $input.metadata.chrom_bed
+--chromosome_windows $input.metadata.chrom_windows
 #if str($hp) == "true":
     --hp true
 #end if
@@ -40,7 +49,7 @@
 #end if
 --input $input
 --input_files_path $input.extra_files_path
---ideas_input_config $input.metadata.ideas_input_config
+--ideas_input_config $input.metadata.input_config
 #if str($log2) != "0.0":
     --log2 $log2
 #end if
@@ -60,6 +69,7 @@
 #if str($minerr) != "0.0":
     --minerr $minerr
 #end if
+--output_dir $output_dir
 #if str($prior_concentration) != "0.0":
     --prior_concentration $prior_concentration
 #end if
@@ -164,6 +174,7 @@
             <param name="initial_states" value="2"/>
             <param name="maxerr" value="1000"/>
             <param name="output_heatmaps" value="no"/>
+            <param name="save_ideas_log" value="yes"/>
             <output_collection name="output_txt_collection" type="list">
                 <element name="IDEAS_out.chr1.cluster" file="IDEAS_out.cluster" ftype="txt"/>
                 <element name="IDEAS_out.chr1.para" file="IDEAS_out.para" ftype="txt"/>