comparison collection_list.Rmd @ 1:6be61cb4a1d5 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty

0:78018b735124

knitr::opts_chunk$set(
  echo = ECHO
)
```

```{r}
str(opt)
```


```{bash 'copy data to working directory', echo=FALSE}
mkdir files_directory
# Copy uploaded data to the working directory
for f in $(echo FILE_LIST | sed "s/,/ /g")
do
    cp $f ./files_directory
done
```

1:6be61cb4a1d5

knitr::opts_chunk$set(
  echo = ECHO
)
```

# Command line arguments

```{r 'command line arguments'}
str(opt)
```


```{r 'rename files'}
# create directory
dir.create('./files_directory')
# get full paths of original files
from_files = strsplit("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', original_files)
# rename files
file.copy(paste0('./files_directory/', original_files),
          paste0('./files_directory/', new_files))
```

# End