Mercurial > repos > devteam > analyze_covariates

comparison analyze_covariates.xml @ 1:e531148fb585 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tool definition that correctly references JAVA_JAR_PATH.
author devteam
date Wed, 02 Apr 2014 14:42:04 -0400
parents 332a7de8f98a
children 7af531c41dd7
comparison
equal deleted inserted replaced
0:332a7de8f98a 1:e531148fb585
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