Mercurial > repos > mingchen0919 > aurora_htseq
changeset 8:1696f5ee0fe7 draft
remove kableextra package
| author | mingchen0919 |
|---|---|
| date | Wed, 18 Apr 2018 17:12:06 -0400 |
| parents | 63cde8d7f89c |
| children | 578a96df8690 |
| files | htseq_count.Rmd htseq_count.xml htseq_count_render.R |
| diffstat | 3 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/htseq_count.Rmd Wed Apr 18 16:11:31 2018 -0400 +++ b/htseq_count.Rmd Wed Apr 18 17:12:06 2018 -0400 @@ -53,7 +53,7 @@ ## Counts -```{r, echo=TRUE} +```{r, echo=FALSE} count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) sample_names = trimws(strsplit(opt$X_B, ',')[[1]]) colnames(count_data) = rep(sample_names, length = ncol(count_data))
--- a/htseq_count.xml Wed Apr 18 16:11:31 2018 -0400 +++ b/htseq_count.xml Wed Apr 18 17:12:06 2018 -0400 @@ -86,8 +86,8 @@ </inputs> <outputs> <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/> - <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/> - <data name="count_rdata" format="rdata" label="${tool.name} count data on ${on_string}"/> + <data name="count" format="txt" label="${tool.name} txt count on ${on_string}" hidden="false"/> + <data name="count_rdata" format="rdata" label="${tool.name} rdata count data on ${on_string}"/> </outputs> <citations> <citation type="bibtex"><![CDATA[
--- a/htseq_count_render.R Wed Apr 18 16:11:31 2018 -0400 +++ b/htseq_count_render.R Wed Apr 18 17:12:06 2018 -0400 @@ -11,8 +11,8 @@ library(getopt) library(rmarkdown) library(htmltools) -library(kableExtra) library(magrittr) +library(knitr) # load helper functions source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R')) # import getopt specification matrix from a csv file