Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat
comparison rmarkdown_samtools_flagstat_render.R @ 5:1c16536c70f5 draft
update
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Dec 2017 15:20:55 -0500 |
| parents | ec39bfeaf496 |
| children |
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| 4:ec39bfeaf496 | 5:1c16536c70f5 |
|---|---|
| 32 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | 32 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| 33 args_list=list() | 33 args_list=list() |
| 34 ##------- 1. input data --------------------- | 34 ##------- 1. input data --------------------- |
| 35 args_list$ECHO = c('echo', 'e', '1', 'character') | 35 args_list$ECHO = c('echo', 'e', '1', 'character') |
| 36 args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character') | 36 args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character') |
| 37 args_list$INPUT_BAM_NAME = c('input_bam_name', 'n', '1', 'character') | |
| 37 ##--------2. output report and outputs -------------- | 38 ##--------2. output report and outputs -------------- |
| 38 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character') | 39 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character') |
| 39 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character') | 40 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character') |
| 40 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character') | 41 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character') |
| 41 ##--------3. .Rmd templates in the tool directory ---------- | 42 ##--------3. .Rmd templates in the tool directory ---------- |