Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
comparison bdss_client_sra_pe_render.R @ 3:c707a4178832 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 11 Oct 2017 11:23:04 -0400 |
| parents | 614e9553f366 |
| children | 206c59e498e7 |
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| 2:979136fc0650 | 3:c707a4178832 |
|---|---|
| 35 # possible values: logical, integer, double, complex, character. | 35 # possible values: logical, integer, double, complex, character. |
| 36 ##------- 1. input data --------------------- | 36 ##------- 1. input data --------------------- |
| 37 spec_list=list() | 37 spec_list=list() |
| 38 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character') | 38 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character') |
| 39 spec_list$FORMAT = c('format', 'f', '1', 'character') | 39 spec_list$FORMAT = c('format', 'f', '1', 'character') |
| 40 spec_list$SRA_BOOLEAN = c('sra_boolean', 'S', '1', 'character') | |
| 40 spec_list$ECHO = c('echo', 'e', '1', 'character') | 41 spec_list$ECHO = c('echo', 'e', '1', 'character') |
| 41 ##--------2. output report and outputs -------------- | 42 ##--------2. output report and outputs -------------- |
| 42 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character') | 43 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character') |
| 43 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') | 44 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') |
| 44 spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') | 45 spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') |
| 69 }) %>% | 70 }) %>% |
| 70 (function(x) { | 71 (function(x) { |
| 71 gsub('FORMAT', opt$format, x) | 72 gsub('FORMAT', opt$format, x) |
| 72 }) %>% | 73 }) %>% |
| 73 (function(x) { | 74 (function(x) { |
| 75 gsub('SRA_BOOLEAN', opt$sra_boolean, x) | |
| 76 }) %>% | |
| 77 (function(x) { | |
| 74 gsub('ECHO', opt$echo, x) | 78 gsub('ECHO', opt$echo, x) |
| 75 }) %>% | 79 }) %>% |
| 76 (function(x) { | 80 (function(x) { |
| 77 gsub('OUTPUT_DIR', opt$output_dir, x) | 81 gsub('OUTPUT_DIR', opt$output_dir, x) |
| 78 }) %>% | 82 }) %>% |