Mercurial > repos > mingchen0919 > elastic_expose_data

annotate list_paired_render.R @ 2:391394c022b8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
author mingchen0919
date Sat, 31 Mar 2018 21:32:17 -0400
parents
children 4f9f1e76f7e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
1 ##============ Sink warnings and errors to a file ==============
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
2 ## use the sink() function to wrap all code within it.
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
3 ##==============================================================
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
4 zz = file(Sys.getenv('TOOL_LOG'))
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
5 sink(zz)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
6 sink(zz, type = 'message')
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
7
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
8 #------------import libraries--------------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
9 options(stringsAsFactors = FALSE)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
10
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
11 library(rmarkdown)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
12 library(stringr)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
13 #------------------------------------------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
14
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
15 #------------------------------------------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
16 options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
17 sep = '|', header = TRUE)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
18
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
19 #------------------------------------------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
20 # create three folders within working directory
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
21 dir.create('list_paired')
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
22
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
23 #-----------------render Rmd--------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
24 # copy R markdown file to working directory and render it within the working directory.
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
25 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list_paired.Rmd'),
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
26 output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
27
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
28 # for some unknow reason, directly using REPORT as the input value for output_file parameter
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
29 # in the render function can cause empty report file when the tool runs in batch mode.
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
30 # the solution is to render the rmarkdown to a explicitly specified file and then copy the
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
31 # file to ${REPORT}
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
32 system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
33 system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
34
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
35 # rename files so that all files have the name pattern BASENAME_forward.EXT and BASENAME_reverse.EXT
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
36 from_files = list.files('list_paired', full.names = TRUE)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
37 to_files = str_replace_all(from_files, c('_1', '_2'), c('_forward', '_reverse'))
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
38 file.rename(from = from_files, to = to_files)
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
39 #------------------------------------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
40
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
41
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
42 ##--------end of code rendering .Rmd templates----------------
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
43 sink()
391394c022b8 planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
mingchen0919
parents:
diff changeset
44 ##=========== End of sinking output=============================