Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 7:2d1c5d1633bf 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 13:41:45 -0400 |
| parents | 4c84d748da08 |
| children | 86a31717730e |
| files | fastq_dump_se_render.R |
| diffstat | 1 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- 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