Mercurial > repos > iuc > gatk2
comparison print_reads.xml @ 2:8bcc13094767 draft
Uploaded
| author | iuc |
|---|---|
| date | Sat, 18 Jan 2014 07:21:33 -0500 |
| parents | 340633249b3d |
| children | f244b8209eb8 |
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| 1:f760c0de8e3a | 2:8bcc13094767 |
|---|---|
| 16 -T "PrintReads" | 16 -T "PrintReads" |
| 17 -o "${output_bam}" | 17 -o "${output_bam}" |
| 18 \$GATK2_SITE_OPTIONS | 18 \$GATK2_SITE_OPTIONS |
| 19 | 19 |
| 20 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 | 20 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 |
| 21 --num_cpu_threads_per_data_thread 8 | 21 --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6} |
| 22 | 22 |
| 23 @THREADS@ | |
| 24 | 23 |
| 25 #if $reference_source.reference_source_selector != "history": | 24 #if $reference_source.reference_source_selector != "history": |
| 26 -R "${reference_source.ref_file.fields.path}" | 25 -R "${reference_source.ref_file.fields.path}" |
| 27 #end if | 26 #end if |
| 28 #if str($input_recal) != 'None': | 27 #if str($input_recal) != 'None': |