Mercurial > repos > devteam > analyze_covariates
comparison analyze_covariates.xml @ 1:1d427770e7ec draft
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 |