Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat
changeset 5:1c16536c70f5 draft
update
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Dec 2017 15:20:55 -0500 |
| parents | ec39bfeaf496 |
| children | f15179ab782b |
| files | rmarkdown_samtools_flagstat.Rmd rmarkdown_samtools_flagstat.xml rmarkdown_samtools_flagstat_render.R |
| diffstat | 3 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/rmarkdown_samtools_flagstat.Rmd Wed Dec 27 15:14:47 2017 -0500 +++ b/rmarkdown_samtools_flagstat.Rmd Wed Dec 27 15:20:55 2017 -0500 @@ -16,7 +16,7 @@ ``` -# Reads alignment stats +# Reads alignment stats on `r opt$input_bam_name` ```{r 'flagstat'} command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
--- a/rmarkdown_samtools_flagstat.xml Wed Dec 27 15:14:47 2017 -0500 +++ b/rmarkdown_samtools_flagstat.xml Wed Dec 27 15:20:55 2017 -0500 @@ -14,6 +14,7 @@ <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R' -e $echo -b $input_bam + -n $input_bam.name -r $report -d $report.files_path -s $sink_message
--- a/rmarkdown_samtools_flagstat_render.R Wed Dec 27 15:14:47 2017 -0500 +++ b/rmarkdown_samtools_flagstat_render.R Wed Dec 27 15:20:55 2017 -0500 @@ -34,6 +34,7 @@ ##------- 1. input data --------------------- args_list$ECHO = c('echo', 'e', '1', 'character') args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character') + args_list$INPUT_BAM_NAME = c('input_bam_name', 'n', '1', 'character') ##--------2. output report and outputs -------------- args_list$REPORT_HTML = c('report_html', 'r', '1', 'character') args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')