Mercurial > repos > jjohnson > defuse
diff defuse.xml @ 27:d57fcac025e2
Add more info fields to defuse_results_to_vcf.py
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 14 Aug 2013 16:44:18 -0500 |
parents | 2ecf82136986 |
children | f51a95bdc38e |
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--- a/defuse.xml Fri Aug 09 11:36:24 2013 -0500 +++ b/defuse.xml Wed Aug 14 16:44:18 2013 -0500 @@ -11,6 +11,9 @@ <inputs> <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/> <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> + <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column"> + <validator type="length" min="1"/> + </param> <conditional name="refGenomeSource"> <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help=""> <option value="indexed">Use a built-in DeFuse Reference Dataset</option> @@ -573,7 +576,7 @@ mkdir -p output_dir #end if ## run defuse.pl -perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p 8 +perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p 8 ## copy primary results to output datasets if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi