Mercurial > repos > mingchen0919 > aurora_dustmasker
diff rmarkdown_report.Rmd @ 1:e0828838e0f3 draft default tip
update
author | mingchen0919 |
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date | Fri, 09 Nov 2018 15:25:01 -0500 |
parents | b8c76b06d724 |
children |
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--- a/rmarkdown_report.Rmd Fri Nov 09 13:29:21 2018 -0500 +++ b/rmarkdown_report.Rmd Fri Nov 09 15:25:01 2018 -0500 @@ -1,5 +1,5 @@ --- -title: 'Aurora Tool Report' +title: 'Dustmasker Report' output: html_document: highlight: pygments @@ -54,23 +54,21 @@ --- -## Run `dustmasker` +## Run `dustmasker` job -```{bash} -dustmasker \ - -in $X_A \ - -window $X_B \ - -level $X_C \ - -linker $X_D \ - -infmt $X_E \ - -outfmt $X_F \ - - $(if [ "$X_G" = "NO_ARGUMENT_YES" ]; then echo '-parse_seqids'; fi) \ - - -out dustmasker_out +```{bash echo=FALSE} +sh ${TOOL_INSTALL_DIR}/scripts_generator.sh ``` -Options explanation: +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/dustmasker.sh')), sep = '\n') +cat('\n```') +``` + + +**Options explanation:** <pre> -in <File_In> @@ -98,5 +96,4 @@ -out <File_Out> output file name - Default = `-' </pre> \ No newline at end of file