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comparison analyze_covariates.xml @ 1:1d427770e7ec draft

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Uploaded tool wrapper XML with correct specification of java .jar path.
author devteam
date Wed, 02 Apr 2014 15:21:06 -0400
parents be6bede22459
children 738bc749f9a3
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0:be6bede22459 1:1d427770e7ec
9 <command interpreter="python">gatk_wrapper.py 9 <command interpreter="python">gatk_wrapper.py
10 --max_jvm_heap_fraction "1" 10 --max_jvm_heap_fraction "1"
11 --stdout "${output_log}" 11 --stdout "${output_log}"
12 --html_report_from_directory "${output_html}" "${output_html.files_path}" 12 --html_report_from_directory "${output_html}" "${output_html.files_path}"
13 -p 'java 13 -p 'java
14 -jar "${JAVA_JAR_PATH}/AnalyzeCovariates.jar" 14 -jar "\$JAVA_JAR_PATH/AnalyzeCovariates.jar"
15 -recalFile "${input_recal}" 15 -recalFile "${input_recal}"
16 -outputDir "${output_html.files_path}" 16 -outputDir "${output_html.files_path}"
17 ##--num_threads 4 ##hard coded, for now 17 ##--num_threads 4 ##hard coded, for now
18 ##-log "${output_log}" 18 ##-log "${output_log}"
19 ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough 19 ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough