Mercurial > repos > jjohnson > cummerbund

diff cuffdiff_wrapper.xml @ 8:fbbbc9fd8fb9

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Use fasta_indexes tool_data_table
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:29:20 -0500
parents b5562b9a55c7
children
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--- a/cuffdiff_wrapper.xml	Mon Oct 13 09:12:47 2014 -0500
+++ b/cuffdiff_wrapper.xml	Mon Oct 13 09:29:20 2014 -0500
@@ -66,7 +66,7 @@
                         &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
                     #else:
                         ## Built-in genome.
-                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
+                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
                     #end if
                 #else 
                     &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r