| Previous changeset 6:137aab1d9ac1 (2013-11-18) Next changeset 8:fbbbc9fd8fb9 (2014-10-13) |
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Commit message:
Use same bias_correction cached param as devteam cuffdiff |
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modified:
cuffdata.py cuffdiff_wrapper.xml |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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> |