Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
comparison fastq_dump_se_render.R @ 6:4c84d748da08 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 11:40:38 -0400 |
| parents | c9b56151f112 |
| children | 2d1c5d1633bf |
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| 5:a2ba5619f51b | 6:4c84d748da08 |
|---|---|
| 60 readLines(opt$fastq_dump_se_rmd) %>% | 60 readLines(opt$fastq_dump_se_rmd) %>% |
| 61 (function(x) { | 61 (function(x) { |
| 62 gsub('SRA_ACCESSION', opt$sra_accession, x) | 62 gsub('SRA_ACCESSION', opt$sra_accession, x) |
| 63 }) %>% | 63 }) %>% |
| 64 (function(x) { | 64 (function(x) { |
| 65 gsub('FORMAT', opt$format, x) | |
| 66 }) %>% | |
| 67 (function(x) { | |
| 65 gsub('ECHO', opt$echo, x) | 68 gsub('ECHO', opt$echo, x) |
| 66 }) %>% | 69 }) %>% |
| 67 (function(x) { | 70 (function(x) { |
| 68 gsub('FORMAT', opt$format, x) | 71 gsub('OUTPUT_DIR', opt$output_dir, x) |
| 69 }) %>% | |
| 70 (function(x) { | |
| 71 gsub('OUTPUT_DIR', opt$fastq_dump_se_dir, x) | |
| 72 }) %>% | 72 }) %>% |
| 73 (function(x) { | 73 (function(x) { |
| 74 fileConn = file('fastq_dump_se.Rmd') | 74 fileConn = file('fastq_dump_se.Rmd') |
| 75 writeLines(x, con=fileConn) | 75 writeLines(x, con=fileConn) |
| 76 close(fileConn) | 76 close(fileConn) |