# HG changeset patch
# User mingchen0919
# Date 1514516833 18000
# Node ID 7857bfd9d6049ae1b26ec229fd95f9a9d73221e7
# Parent  a2bf35c1974afcf504525212582f72929eec8d7c
update

diff -r a2bf35c1974a -r 7857bfd9d604 rmarkdown_feature_counts.Rmd
--- a/rmarkdown_feature_counts.Rmd	Thu Dec 28 16:56:01 2017 -0500
+++ b/rmarkdown_feature_counts.Rmd	Thu Dec 28 22:07:13 2017 -0500
@@ -10,7 +10,7 @@
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = ECHO,
+  echo = opt$echo,
   error = TRUE
 )
 ```
@@ -19,7 +19,7 @@
 # Code for computational analysis
 
 ```{r 'step 1'}
-
+opt
 ```
 
 ```{r 'ste[ 2'}
diff -r a2bf35c1974a -r 7857bfd9d604 rmarkdown_feature_counts.xml
--- a/rmarkdown_feature_counts.xml	Thu Dec 28 16:56:01 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 22:07:13 2017 -0500
@@ -15,6 +15,40 @@
     <command><![CDATA[
                     Rscript '${__tool_directory__}/rmarkdown_feature_counts_render.R'
                         -e $echo
+                        -a $input_bam
+                        -b $annot_inbuilt
+                        -c '$annot_ext'
+                        -f $isGTFAnnotationFile
+                        -g $gtf_feature_type
+                        -h $gtf_attr_type
+                        -i $chr_aliases
+                        -j $use_meta_features
+                        -k $allow_multi_overlap
+                        -l $min_overlap
+                        -m $largest_overlap
+                        -n $read_extension_5
+                        -o $read_extension_3
+                        -p $read_2_pos
+                        -q $count_multi_mapping_reads
+                        -u $fraction
+                        -v $min_mqs
+                        -w $split_only
+                        -x $non_split_only
+                        -y $primary_only
+                        -z $ignore_dup
+                        -A $strand_specific
+                        -B $junc_counts
+                        -C $genome
+                        -D $is_paired_end
+                        -E $require_both_ends_mapped
+                        -F $check_frag_length
+                        -G $min_frag_length
+                        -H $max_frag_length
+                        -I $count_chimeric_fragments
+                        -J $auto_sort
+                        -K $n_threads
+                        -L $max_mop
+                        -M $report_reads
                         -r $report
                         -d $report.files_path
                         -s $sink_message
diff -r a2bf35c1974a -r 7857bfd9d604 rmarkdown_feature_counts_render.R
--- a/rmarkdown_feature_counts_render.R	Thu Dec 28 16:56:01 2017 -0500
+++ b/rmarkdown_feature_counts_render.R	Thu Dec 28 22:07:13 2017 -0500
@@ -2,6 +2,7 @@
 library(rmarkdown)
 library(htmltools)
 library(dplyr)
+library(Rsubread)
 
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
@@ -32,6 +33,40 @@
   args_list=list()
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
+  args_list$b = c('input_bam', 'b', '1', 'character')
+  args_list$c = c('annot_ext', 'c', '1', 'character')
+  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'character')
+  args_list$g = c('gtf_feature_type', 'g', '1', 'character')
+  args_list$h = c('gtf_attr_type', 'h', '1', 'character')
+  args_list$i = c('chr_aliases', 'i', '1', 'character')
+  args_list$j = c('use_meta_features', 'j', '1', 'character')
+  args_list$k = c('allow_multi_overlap', 'k', '1', 'character')
+  args_list$l = c('min_overlap', 'l', '1', 'character')
+  args_list$m = c('largest_overlap', 'm', '1', 'character')
+  args_list$n = c('read_extension_5', 'n', '1', 'character')
+  args_list$o = c('read_extension_3', 'o', '1', 'character')
+  args_list$p = c('read_2_pos', 'p', '1', 'character')
+  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'character')
+  args_list$u = c('fraction', 'u', '1', 'character')
+  args_list$v= c('min_mqs', 'v', '1', 'character')
+  args_list$w= c('split_only', 'w', '1', 'character')
+  args_list$x= c('non_split_only', 'x', '1', 'character')
+  args_list$y= c('primary_only', 'y', '1', 'character')
+  args_list$z= c('ignore_dup', 'z', '1', 'character')
+  args_list$A= c('strand_specific', 'A', '1', 'character')
+  args_list$B= c('junc_counts', 'B', '1', 'character')
+  args_list$C= c('genome', 'C', '1', 'character')
+  args_list$D= c('is_paired_end', 'D', '1', 'character')
+  args_list$E= c('require_both_ends_mapped', 'E', '1', 'character')
+  args_list$F= c('check_frag_length', 'F', '1', 'character')
+  args_list$G= c('min_frag_length', 'G', '1', 'character')
+  args_list$H= c('max_frag_length', 'H', '1', 'character')
+  args_list$I= c('count_chimeric_fragments', 'I', '1', 'character')
+  args_list$J= c('auto_sort', 'J', '1', 'character')
+  args_list$K= c('n_threads', 'K', '1', 'character')
+  args_list$L= c('max_mop', 'L', '1', 'character')
+  args_list$M= c('report_reads', 'M', '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')