changeset 4:ec39bfeaf496 draft

update

--- a/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 12:03:33 2017 -0500
+++ b/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 15:14:47 2017 -0500
@@ -1,5 +1,5 @@
 ---
-title: 'HTML report title'
+title: 'Reads alignment stats'
 output:
     html_document:
       number_sections: true
@@ -16,13 +16,17 @@
 ```
 
 
-# Code for computational analysis
+# Reads alignment stats
 
-```{r 'step 1'}
-command = paste0('samtools flagstat ', opt$input_bam, ' > report.csv')
+```{r 'flagstat'}
+command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
 system(command)
-read.csv('report.csv')
+df = readLines(paste0(opt$report_dir, '/report.txt')) %>%
+  str_replace('(\\d+\\s+\\+\\s+\\d+)\\s+', '\\1,') %>% 
+  str_split(',') %>% 
+  as.data.frame() %>% t()
+rownames(df) = NULL
+colnames(df) = c('PASS + FAIL', 'Description')
+knitr::kable(df)
 ```
 
-
-

--- a/rmarkdown_samtools_flagstat.xml	Wed Dec 27 12:03:33 2017 -0500
+++ b/rmarkdown_samtools_flagstat.xml	Wed Dec 27 15:14:47 2017 -0500
@@ -11,13 +11,13 @@
   <stdio>
     <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
   </stdio>
-  <command><![CDATA[                    Rscript '${__tool_directory__}/tool_template_render.R'
+  <command><![CDATA[                    Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
                         -e $echo
                         -b $input_bam
                         -r $report
                         -d $report.files_path
                         -s $sink_message
-                        -t '${__tool_directory__}/tool_template.Rmd'
+                        -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>

--- a/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 12:03:33 2017 -0500
+++ b/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 15:14:47 2017 -0500
@@ -2,6 +2,7 @@
 library(rmarkdown)
 library(htmltools)
 library(dplyr)
+library(stringr)
 
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
@@ -58,10 +59,10 @@
       gsub('ECHO', opt$echo, x)
     }) %>%
     (function(x) {
-      gsub('REPORT_DIR', opt$output_dir, x)
+      gsub('REPORT_DIR', opt$report_dir, x)
     }) %>%
     (function(x) {
-      fileConn = file('tool_template.Rmd')
+      fileConn = file('rmarkdown_samtools_flagstat.Rmd')
       writeLines(x, con=fileConn)
       close(fileConn)
     })
@@ -70,7 +71,7 @@
   ##=============STEP 4: render .Rmd templates=================
   ##
   ##===========================================================
-  render('tool_template.Rmd', output_file = opt$report_html)
+  render('rmarkdown_samtools_flagstat.Rmd', output_file = opt$report_html)
 
 
   ##--------end of code rendering .Rmd templates----------------