# HG changeset patch
# User mingchen0919
# Date 1506534105 14400
# Node ID 2d1c5d1633bfa65d8f120ae3f8586f9c3011f726
# Parent  4c84d748da0840006e47e1ad5109860a1c99464d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty

diff -r 4c84d748da08 -r 2d1c5d1633bf fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Sep 27 11:40:38 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Sep 27 13:41:45 2017 -0400
@@ -20,6 +20,9 @@
   library(tools)
 })
 
+#/////////////////////// SINK OUTPUTS TO A FILE FOR DEBUGGING ///////////
+sink('sink_output.txt')
+
 # column 1: the long flag name
 # column 2: the short flag alias. A SINGLE character string
 # column 3: argument mask
@@ -34,8 +37,9 @@
 spec_list$FORMAT = c('format', 'f', '1', 'character')
 spec_list$ECHO = c('echo', 'e', '1', 'character')
 ##--------2. output report and outputs --------------
-spec_list$FASTQ_DUMP_SE_HTML = c('fastq_dump_se_html', 'r', '1', 'character')
+spec_list$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')
 ##--------3. Rmd templates in the tool directory ----------
 spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_se_rmd', 't', '1', 'character')
 
@@ -77,7 +81,14 @@
   })
 
 #------ 3. render all Rmd files --------
-render('fastq_dump_se.Rmd', output_file = opt$fastq_dump_se_html)
+render('fastq_dump_se.Rmd', output_file = opt$report_html)
+
+
+#-------4. manipulate outputs -----------------------------
 
 
-#-------4. manipulate outputs -----------------------------
\ No newline at end of file
+
+
+
+sink()
+#/////////// END OF SINK OUTPUT ///////////////////////////
\ No newline at end of file