diff 01_evaluation_overview.Rmd @ 7:3f92c10de274 draft

planemo upload

--- a/01_evaluation_overview.Rmd	Tue Mar 13 11:33:13 2018 -0400
+++ b/01_evaluation_overview.Rmd	Mon Apr 30 10:15:54 2018 -0400
@@ -18,69 +18,17 @@
 
 # Run FastQC
 
-```{bash eval=TRUE,echo=FALSE}
-cd ${X_d}
-cp ${X_r} ${X_d}/read_1.fq
-cp ${X_R} ${X_d}/read_2.fq
-
-mkdir -p read_1 read_2
-cat >temp.sh <<EOL
-fastqc \\
-  -q \\
-  -c ${X_c} \\
-  -l ${X_l} \\
-  ${X_d}/read_1.fq > /dev/null 2>&1
-  
-fastqc \\
-  -q \\
-  -c ${X_c} \\
-  -l ${X_l} \\
-  ${X_d}/read_2.fq > /dev/null 2>&1
-EOL
-
-grep -v None temp.sh > fastqc.sh
-
-# run fastqc
-sh fastqc.sh
-
-# unzip outputs
-unzip -q read_1_fastqc.zip
-unzip -q read_2_fastqc.zip
+```{bash}
+sh ${TOOL_INSTALL_DIR}/shell-script-template.sh
 ```
 
-```{r}
+```{r echo=FALSE,results='asis'}
 # display fastqc job script
-fastqc_sh = paste0(opt$X_d, '/fastqc.sh')
-tags$code(tags$pre(readChar(fastqc_sh, file.info(fastqc_sh)$size )))
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastqc.sh')), sep = '\n')
+cat('\n```')
 ```
 
-# Raw FastQC reports
-
-## Before trimming
-```{r eval=TRUE}
-ori_html = tags$a(href = 'read_1_fastqc/fastqc_report.html', opt$X_n)
-ori_fastqc_data = tags$a(href = 'read_1_fastqc/fastqc_data.txt', 'fastqc_data.txt')
-ori_summary = tags$a(href = 'read_1_fastqc/summary.txt', 'summary.txt')
-tags$ul(
-    tags$li(ori_html),
-    tags$li(ori_fastqc_data),
-    tags$li(ori_summary)
-  )
-```
-
-## After trimming
-```{r eval=TRUE}
-ori_html = tags$a(href = 'read_2_fastqc/fastqc_report.html', opt$X_n)
-ori_fastqc_data = tags$a(href = 'read_2_fastqc/fastqc_data.txt', 'fastqc_data.txt')
-ori_summary = tags$a(href = 'read_2_fastqc/summary.txt', 'summary.txt')
-tags$ul(
-    tags$li(ori_html),
-    tags$li(ori_fastqc_data),
-    tags$li(ori_summary)
-  )
-```
-
-
 # Fastqc Output Visualization
 
 ## Overview