# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413209567 18000
# Node ID b5562b9a55c76b3c31e843181e0d28b3b6cdd070
# Parent  137aab1d9ac11be1da4ee5246445c96c59675f36
Use same bias_correction cached param as devteam cuffdiff

diff -r 137aab1d9ac1 -r b5562b9a55c7 cuffdata.py
--- a/cuffdata.py	Mon Nov 18 16:43:15 2013 -0600
+++ b/cuffdata.py	Mon Oct 13 09:12:47 2014 -0500
@@ -135,8 +135,7 @@
             ## Create a tmpdir
             ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids
             ## define file names to use as sinks for each type of data
-            # tmp_dir = tempfile.mkdtemp()
-            tmp_dir = '/tmp/gx/cuffdb'
+            tmp_dir = tempfile.mkdtemp()
             if not os.path.isdir(tmp_dir):
                 os.makedirs(tmp_dir)
             rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name
diff -r 137aab1d9ac1 -r b5562b9a55c7 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Mon Nov 18 16:43:15 2013 -0600
+++ b/cuffdiff_wrapper.xml	Mon Oct 13 09:12:47 2014 -0500
@@ -40,7 +40,7 @@
                     $bias_correction.seq_source.ref_file
                 #else:
                     ## Built-in genome.
-                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
+                    ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
             #end if
 
@@ -123,7 +123,14 @@
                     <option value="cached">Locally cached</option>
                     <option value="history">History</option>
                   </param>
-                  <when value="cached"></when>
+                  <when value="cached">
+                    <param name="index" type="select" label="Using reference genome">
+                      <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
+                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+                      </options>
+                    </param>
+                  </when>
                   <when value="history">
                       <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                   </when>