# HG changeset patch
# User greg
# Date 1510942407 18000
# Node ID cfa683d96cae6014bad12e6e2f58c24532ba34d0
# Parent  1d99221369b128caba57801eabc4aea23af4102e
Uploaded

diff -r 1d99221369b1 -r cfa683d96cae ideas.xml
--- a/ideas.xml	Fri Nov 17 11:39:15 2017 -0500
+++ b/ideas.xml	Fri Nov 17 13:13:27 2017 -0500
@@ -9,7 +9,8 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set output_dir = "output_dir"
+#set output_pdf_dir = "output_pdf_dir"
+#set output_txt_dir = "output_txt_dir"
 #set tmp_dir = "tmp"
 #set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = "prep_output_config.txt"
@@ -17,7 +18,8 @@
 ## Create the config file and prepare the data
 ##############################################
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-mkdir '$output_dir' &&
+mkdir '$output_pdf_dir' &&
+mkdir '$output_txt_dir' &&
 cp '$gen_prep_input_config' $prep_input_config &&
 prepMat
 $prep_input_config
@@ -94,13 +96,13 @@
 #else:
     > /dev/null
 #end if
-&& mv ./*.cluster '$output_dir'
-&& mv ./*.para '$output_dir'
-&& mv ./*.profile '$output_dir'
-&& mv ./*.state '$output_dir'
+&& mv ./*.cluster '$output_txt_dir'
+&& mv ./*.para '$output_txt_dir'
+&& mv ./*.profile '$output_txt_dir'
+&& mv ./*.state '$output_txt_dir'
 && Rscript '$__tool_directory__/create_heatmap.R'
--i '$output_dir/myProject.para'
--o '$output_heatmap'
+-i '$output_txt_dir'
+-o '$output_pdf_dir'
     ]]></command>
     <configfiles>
         <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
@@ -210,9 +212,11 @@
         <data name="output_log" format="txt" label="${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_pdf_collection" type="list">
+            <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/>
+        </collection>
         <collection name="output_txt_collection" type="list">
-            <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
+            <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/>
         </collection>
     </outputs>
     <tests>
@@ -225,11 +229,13 @@
             <param name="project_name" value="IDEAS_out"/>
             <output_collection name="output_txt_collection" type="list">
                 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
-                <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
+                <element name="IDEAS_out.para" file="IDEAS_out.para" ftype="txt"/>
                 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
                 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
             </output_collection>
-            <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
+            <output_collection name="output_pdf_collection" type="list">
+                <element name="something.pdf" file="IDEAS_out.cluster" compare="contains"/>
+            </output_collection>
         </test>
         <test>
             <param name="cell_type_epigenetic_factor" value="manual"/>
@@ -243,11 +249,13 @@
             <param name="project_name" value="IDEAS_out"/>
             <output_collection name="output_txt_collection" type="list">
                 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
-                <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
+                <element name="IDEAS_out.para" file="IDEAS_out.para" ftype="txt"/>
                 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
                 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
             </output_collection>
-            <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
+            <output_collection name="output_pdf_collection" type="list">
+                <element name="something.pdf" file="IDEAS_out.cluster" compare="contains"/>
+            </output_collection>
         </test>
     </tests>
     <help>