Mercurial > repos > jjohnson > cummerbund
comparison cuffdiff_wrapper.xml @ 8:fbbbc9fd8fb9
Use fasta_indexes tool_data_table
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 13 Oct 2014 09:29:20 -0500 |
| parents | b5562b9a55c7 |
| children |
comparison
equal
deleted
inserted
replaced
| 7:b5562b9a55c7 | 8:fbbbc9fd8fb9 |
|---|---|
| 64 #if $bias_correction.seq_source.index_source == "history": | 64 #if $bias_correction.seq_source.index_source == "history": |
| 65 ## Custom genome from history. | 65 ## Custom genome from history. |
| 66 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r | 66 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r |
| 67 #else: | 67 #else: |
| 68 ## Built-in genome. | 68 ## Built-in genome. |
| 69 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r | 69 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r |
| 70 #end if | 70 #end if |
| 71 #else | 71 #else |
| 72 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r | 72 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r |
| 73 #end if | 73 #end if |
| 74 && Rscript --vanilla cuffData.r | 74 && Rscript --vanilla cuffData.r |