# HG changeset patch
# User greg
# Date 1517929774 18000
# Node ID a4e4ca3c021d0fe9c97c3eb60099af9c45f78603
# Parent  28a995056cd0df540f2c8b1ff9cea8091d992df7
Uploaded

diff -r 28a995056cd0 -r a4e4ca3c021d ideas.xml
--- a/ideas.xml	Mon Feb 05 14:32:53 2018 -0500
+++ b/ideas.xml	Tue Feb 06 10:09:34 2018 -0500
@@ -13,10 +13,8 @@
 #import os
 #set perform_training = $perform_training_cond.perform_training
 
-## Copy the input's compressed tmp directory archive.
-cp $input.metadata.tmp_archive . &&
-## Extract the tmp archive.
-tar -xzf tmp.tar.gz &&
+## Extract the input's compressed tmp directory archive.
+tar -xzf $input.metadata.tmp_archive &&
 
 ## Define and create output directories.
 #set output_pdf_dir = "output_pdf_dir"
@@ -173,6 +171,12 @@
             <param name="training_iterations" value="3"/>
             <param name="input" value="ideas_test1/input.html" dbkey="hg19" ftype="ideaspre">
                 <composite_data value='ideas_test1/chromosomes.bed' dbkey="hg19"/>
+                <!--
+                    There seems to be a bug in the Galaxy upload form for composite datatypes
+                    in that even optional files are required.  The chromosome_windows.txt
+                    file is optional for the IdeasPre datatype, but we have to include it
+                    here due to this bug.
+                -->
                 <composite_data value='ideas_test1/chromosome_windows.txt' dbkey="hg19"/>
                 <composite_data value='ideas_test1/IDEAS_input_config.txt' dbkey="hg19"/>
                 <composite_data value='ideas_test1/tmp.tar.gz' dbkey="hg19"/>