Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
diff fastq_dump_pe_render.R @ 13:66bc1016ec2a draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
author | mingchen0919 |
---|---|
date | Wed, 27 Sep 2017 16:54:07 -0400 |
parents | d4a9c31d0046 |
children | 627c487d22e3 |
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--- a/fastq_dump_pe_render.R Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_pe_render.R Wed Sep 27 16:54:07 2017 -0400 @@ -38,11 +38,10 @@ spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') -spec_list$SPLIT_FILES = c('split_files', 'p', '1', 'character') ##--------2. output report and outputs -------------- spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') -spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character') +spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character') @@ -75,9 +74,6 @@ gsub('ECHO', opt$echo, x) }) %>% (function(x) { - gsub('SPLIT_FILES', opt$split_files, x) - }) %>% - (function(x) { gsub('OUTPUT_DIR', opt$output_dir, x) }) %>% (function(x) {