diff fastq_dump_pe.Rmd @ 11:d4a9c31d0046 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

--- a/fastq_dump_pe.Rmd	Wed Sep 27 16:17:40 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 16:43:52 2017 -0400
@@ -0,0 +1,48 @@
+---
+title: 'Fastq-dump: download and extract paired end reads into FASTQ/FASTA file'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO
+)
+```
+
+# Command line arguments
+
+```{r 'command line arguments'}
+str(opt)
+```
+
+# Download and extract reads
+
+```{r 'download and extract reads'}
+# create a directory to store read files
+dir.create('read_files_directory')
+# download and extract reads
+sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
+sra_accessions = sra_accessions[sra_accessions != '']
+# loop through SRA accessions to download and extract reads.
+for(id in sra_accessions) {
+  if('FORMAT' == 'fasta') {
+    command = paste0('fastq-dump --fasta ', '-O read_files_directory ')
+  } else {
+    command = paste0('fastq-dump ', '-O read_files_directory ')
+  }
+  
+  if('SPLIT_FILES' == TRUE) {
+    command = paste0(command, '--split_files ', id)
+  } else {
+    command = paste0(command, id)
+  }
+  print(command)
+  system(command = command)
+}
+```
+