view collection_list_paired.Rmd @ 17:2f6a7c67440f draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty

---
title: 'Collection builder (collection type: list:paired)'
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)
```

# Rename files

## Forward inputs

```{r 'create inputs directory'}
# create directory
dir.create('./files_directory')
```

```{r 'rename forward files'}
# get full paths of original files
from_files = strsplit("FOWARD_FILE_LIST", ',')[[1]]
# copy files to the created directory.
file.copy(from_files, './files_directory')
# get original file names
original_files = list.files('./files_directory')
# create new files names from original file names
new_files = gsub('\\.dat', '\\.FORMAT_1', original_files)
# rename files
file.copy(paste0('./files_directory/', original_files),
          paste0('./files_directory/', new_files))
```

## Reverse inputs

```{r 'rename reverse files'}
# get full paths of original files
from_files = strsplit("FOWARD_FILE_LIST", ',')[[1]]
# copy files to the created directory.
file.copy(from_files, './files_directory')
# get original file names
original_files = list.files('./files_directory')
# create new files names from original file names
new_files = gsub('\\.dat', '\\.FORMAT_2', original_files)
# rename files
file.copy(paste0('./files_directory/', original_files),
          paste0('./files_directory/', new_files))
```