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comparison print_reads.xml @ 2:8bcc13094767 draft

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Uploaded
author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
comparison
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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':