annotate fastq_dump_se.Rmd @ 0:1a11c4fd13d0 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b

---
title: 'Fastq-dump: download and extract single 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 ', id)
  } else {
    command = paste0('fastq-dump ', '-O read_files_directory ', id)
  }
}
```

* `fastq-dump` command
```{r}
print(command)
```

* `command line stdout`

```{r}
system(command = command, intern = TRUE)
```