Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list_paired.Rmd @ 5:66022ba24ac7 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
author mingchen0919
date Tue, 26 Sep 2017 00:16:09 -0400
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children a0c8b2b25774
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4:63e9500cdeec 5:66022ba24ac7
1 ---
2 title: 'Collection builder (collection type: list:paired)'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = ECHO
14 )
15 ```
16
17 # Command line arguments
18
19 ```{r 'command line arguments'}
20 str(opt)
21 ```
22
23 # Rename files
24
25 ## Forward inputs
26
27 ```{r 'create inputs directory'}
28 # create directory to store both forward and reverse inputs
29 # this is the directory where datasets will be discovered.
30 dir.create('./files_directory')
31 ```
32
33 ```{r 'rename forward files'}
34 # create directory
35 dir.create('./forward_files_directory')
36 # get full paths of original files
37 from_files = strsplit("FORWARD_FILE_LIST", ',')[[1]]
38 # copy files to forward_files_directory.
39 file.copy(from_files, './forward_files_directory')
40 # get original file names
41 original_files = list.files('./forward_files_directory')
42 # create new files names from original file names
43 new_files = gsub('\\.dat', '_forward\\.FORMAT', original_files)
44 new_files = paste0('input_', 1:length(original_files), '_forward.FORMAT')
45 new_files
46 # rename files
47 file.copy(paste0('./forward_files_directory/', original_files),
48 paste0('./files_directory/', new_files))
49 ```
50
51 ## Reverse inputs
52
53 ```{r 'rename reverse files'}
54 # create directory
55 dir.create('./reverse_files_directory')
56 # get full paths of original files
57 from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]]
58 # copy files to reverse_files_directory.
59 file.copy(from_files, './reverse_files_directory')
60 # get original file names
61 original_files = list.files('./reverse_files_directory')
62 # create new files names from original file names
63 new_files = gsub('\\.dat', '_reverse\\.FORMAT', original_files)
64 new_files = paste0('input_', 1:length(original_files), '_reverse.FORMAT')
65 new_files
66 # rename files
67 file.copy(paste0('./reverse_files_directory/', original_files),
68 paste0('./files_directory/', new_files))
69 ```
70