# HG changeset patch
# User mingchen0919
# Date 1514406055 18000
# Node ID 1c16536c70f5556cc7a3bbd5d66b95d14171b619
# Parent  ec39bfeaf49654d5385506ef38b47f838df0d314
update

diff -r ec39bfeaf496 -r 1c16536c70f5 rmarkdown_samtools_flagstat.Rmd
--- a/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 15:14:47 2017 -0500
+++ b/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 15:20:55 2017 -0500
@@ -16,7 +16,7 @@
 ```
 
 
-# Reads alignment stats
+# Reads alignment stats on `r opt$input_bam_name`
 
 ```{r 'flagstat'}
 command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
diff -r ec39bfeaf496 -r 1c16536c70f5 rmarkdown_samtools_flagstat.xml
--- a/rmarkdown_samtools_flagstat.xml	Wed Dec 27 15:14:47 2017 -0500
+++ b/rmarkdown_samtools_flagstat.xml	Wed Dec 27 15:20:55 2017 -0500
@@ -14,6 +14,7 @@
   <command><![CDATA[                    Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
                         -e $echo
                         -b $input_bam
+                        -n $input_bam.name
                         -r $report
                         -d $report.files_path
                         -s $sink_message
diff -r ec39bfeaf496 -r 1c16536c70f5 rmarkdown_samtools_flagstat_render.R
--- a/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 15:14:47 2017 -0500
+++ b/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 15:20:55 2017 -0500
@@ -34,6 +34,7 @@
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
   args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character')
+  args_list$INPUT_BAM_NAME = c('input_bam_name', 'n', '1', 'character')
   ##--------2. output report and outputs --------------
   args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
   args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')