Mercurial > repos > mingchen0919 > elastic_expose_data
annotate individuals.Rmd @ 7:23cbb0daf18d draft default tip
planemo upload commit d1d9c6fc42729b4194adac13d1b71062bf19ad0b-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 02 Apr 2018 10:53:05 -0400 |
| parents | 4f9f1e76f7e6 |
| children |
| rev | line source |
|---|---|
| 3 | 1 --- |
| 2 title: 'Expose data (paired)' | |
| 3 output: html_document | |
| 4 --- | |
| 5 | |
| 6 <style> | |
| 7 pre code, pre, code { | |
| 8 white-space: pre !important; | |
| 9 overflow-x: scroll !important; | |
| 10 word-break: keep-all !important; | |
| 11 word-wrap: initial !important; | |
| 12 } | |
| 13 </style> | |
| 14 | |
| 15 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
| 16 knitr::opts_chunk$set(error = TRUE) | |
| 17 ``` | |
| 18 | |
| 19 ## User input | |
| 20 | |
| 21 ```{r, echo=FALSE, eval=TRUE} | |
| 22 ##-------- build script files ----------- | |
| 23 | |
| 24 # build script file: script.sh | |
| 25 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), | |
| 26 sep = '|', header = TRUE) | |
| 27 | |
| 28 | |
| 29 knitr::kable(df) | |
| 30 ``` | |
| 31 | |
| 32 ```{r, echo=FALSE} | |
| 33 # write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) | |
| 34 if (nrow(df) > 0) { | |
| 35 for (i in 1:nrow(df)) { | |
| 36 tool_output_dir = readLines(df[i, 'tool_output_dir'])[1] | |
| 37 full_path = paste0(tool_output_dir, '/', df[i, 'relative_path']) | |
| 38 if (dir.exists(full_path)) { | |
| 39 from_files = list.files(full_path, full.names = TRUE) | |
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9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
40 to_files = list.files(full_path) |
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9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
41 to_files = paste0(individual_outputs_path, to_files) |
| 3 | 42 file.copy(from = from_files, to = to_files) |
| 43 } | |
| 44 if (file.exists(full_path)) { | |
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4
9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
45 # to_files = list.files(full_path) |
|
9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
46 to_file = tail(strsplit(full_path, '/')[[1]], 1) |
|
9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
47 file.copy(from = full_path, to = paste0(individual_outputs_path, to_file)) |
| 3 | 48 } |
| 49 # command_line = paste0('cp -r ', full_path, ' paired') | |
| 50 # write(command_line, append = TRUE, | |
| 51 # file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) | |
| 52 } | |
| 53 } | |
| 54 ``` | |
| 55 | |
| 56 |