# HG changeset patch
# User mingchen0919
# Date 1524085926 14400
# Node ID 1696f5ee0fe73307d128e18d2fb5f889d13e7a86
# Parent  63cde8d7f89c47c3b9aea7703662cf91d34fd999
remove kableextra package

diff -r 63cde8d7f89c -r 1696f5ee0fe7 htseq_count.Rmd
--- 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))
diff -r 63cde8d7f89c -r 1696f5ee0fe7 htseq_count.xml
--- 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[
diff -r 63cde8d7f89c -r 1696f5ee0fe7 htseq_count_render.R
--- 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