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

--- 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) {