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comparison reduce_reads.xml @ 10:a14e79e7ac75 draft

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Comment out site options from reduce_reads.xml
author Jim Johnson <jj@umn.edu>
date Tue, 06 Nov 2012 12:07:36 -0600
parents f253357915e0
children 5faf7ace8aee
comparison
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9:24504f5cac5e 10:a14e79e7ac75
13 #end if 13 #end if
14 -p 'java 14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "ReduceReads" 16 -T "ReduceReads"
17 -o "${output_bam}" 17 -o "${output_bam}"
18 \$GATK2_SITE_OPTIONS 18 ## \$GATK2_SITE_OPTIONS
19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home 19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
20 ##--num_threads 4 ##not supported yet 20 ##--num_threads 4 ##not supported yet
21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
22 #if $reference_source.reference_source_selector != "history": 22 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}" 23 -R "${reference_source.ref_file.fields.path}"