# HG changeset patch
# User greg
# Date 1510673695 18000
# Node ID a0e38f759ad576322696e357d39a85ea00b414d0
# Parent  14659ab1e709f01b3fd8f910c7f70da914b92528
Uploaded

diff -r 14659ab1e709 -r a0e38f759ad5 ideas.xml
--- a/ideas.xml	Tue Nov 14 10:34:47 2017 -0500
+++ b/ideas.xml	Tue Nov 14 10:34:55 2017 -0500
@@ -6,7 +6,7 @@
         <requirement type="package" version="332">ucsc-bedsort</requirement>
         <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
         <requirement type="package" version="1.20">ideas</requirement>
-        <requirement type="package" version="1.3.2">r-optparse</requirement>
+        <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set output_dir = "output_dir"
@@ -17,7 +17,7 @@
 ## Create the config file and prepare the data
 ##############################################
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-mkdir $output_dir &&
+mkdir '$output_dir' &&
 cp '$gen_prep_input_config' $prep_input_config &&
 prepMat
 $prep_input_config
@@ -97,10 +97,12 @@
 && mv ./*.para '$output_dir'
 && mv ./*.profile '$output_dir'
 && mv ./*.state '$output_dir'
+&& Rscript '$__tool_directory__/create_heatmap.R'
+-i '$output_dir/*.para'
+-o '$output_heatmap'
     ]]></command>
     <configfiles>
-        <configfile name="gen_prep_input_config"><![CDATA[#import os
-#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
+        <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
     #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
     #for $i in $cell_type_epigenetic_factor_cond.input:
         #set file_name_with_ext = $i.name
@@ -204,6 +206,7 @@
         <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
             <filter>save_ideas_log == 'yes'</filter>
         </data>
+        <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/>
         <collection name="output" type="list">
             <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
         </collection>
@@ -224,7 +227,6 @@
                 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
                 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
             </output_collection>
-
         </test>
         <test>
             <param name="cell_type_epigenetic_factor" value="manual"/>