Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db-dirty
author mingchen0919
date Tue, 26 Sep 2017 16:23:47 -0400
parents 2556fed6c3c7
children
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1 ---
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2 title: 'Build collection: a list of paired datasets'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = ECHO
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14 )
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15 ```
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17 # Command line arguments
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19 ```{r 'command line arguments'}
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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20 str(opt)
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21 ```
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23 # Rename files
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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25 ## Forward inputs
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27 ```{r 'create inputs directory'}
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28 # create directory to store both forward and reverse inputs
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29 # this is the directory where datasets will be discovered.
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30 dir.create('./files_directory')
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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31 ```
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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33 ```{r 'rename forward files'}
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34 # create directory
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35 dir.create('./forward_files_directory')
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36 # get full paths of original files
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37 from_files = strsplit("FORWARD_FILE_LIST", ',')[[1]]
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38 # copy files to forward_files_directory.
975365a3e126 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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39 file.copy(from_files, './forward_files_directory')
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40 # get original file names
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41 original_files = list.files('./forward_files_directory')
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42 # create new files names from original file names
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43 new_files = paste0('input', 1:length(original_files), '_forward.FORMAT')
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44 # rename files
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45 file.copy(paste0('./forward_files_directory/', original_files),
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46 paste0('./files_directory/', new_files))
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47 ```
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49 ## Reverse inputs
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51 ```{r 'rename reverse files'}
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52 # create directory
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53 dir.create('./reverse_files_directory')
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54 # get full paths of original files
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55 from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]]
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56 # copy files to reverse_files_directory.
975365a3e126 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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57 file.copy(from_files, './reverse_files_directory')
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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58 # get original file names
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59 original_files = list.files('./reverse_files_directory')
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60 # create new files names from original file names
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61 new_files = paste0('input', 1:length(original_files), '_reverse.FORMAT')
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62 # rename files
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63 file.copy(paste0('./reverse_files_directory/', original_files),
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64 paste0('./files_directory/', new_files))
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65 ```