Mercurial > repos > jjohnson > cummerbund
diff cuffdiff_wrapper.xml @ 3:f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 15 Nov 2013 13:39:14 -0600 |
| parents | fdf01b3c1841 |
| children | b5562b9a55c7 |
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--- a/cuffdiff_wrapper.xml Fri Nov 08 14:54:01 2013 -0600 +++ b/cuffdiff_wrapper.xml Fri Nov 15 13:39:14 2013 -0600 @@ -58,13 +58,15 @@ #if $build_cummerbund_db: && echo 'library(cummeRbund)' > cuffData.r #if $bias_correction.do_bias_correction == "Yes": + ## cummeRbund relies on the file extension to determine gff format + #set $gtf_link = '.'.join(['cuff',$gtf_input.extension]) + && ln -s $gtf_input $gtf_link #if $bias_correction.seq_source.index_source == "history": ## Custom genome from history. - && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r + && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r #else: ## Built-in genome. - ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} - && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r + && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r #end if #else && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r @@ -134,7 +136,9 @@ <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> - <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/> + <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"> + <help>"Perform Bias Correction" must be selected to include gtf and genome reference in the cummeRbund database.</help> + </param> <conditional name="additional"> <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)"> <option value="No">No</option>