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comparison dynamic_tool.Rmd @ 2:a9579c344a90 draft default tip

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planemo upload commit 8f84e3911c6ff4103c0ad5fb8dd774f80d9b2559
author mingchen0919
date Fri, 23 Mar 2018 21:50:16 -0400
parents d79569f269c7
children
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1:ddc3c3527f49 2:a9579c344a90
1 --- 1 ---
2 title: 'Dynamic tool' 2 title: 'Dynamic tool'
3 output: html_document 3 output: html_document
4 --- 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>
5 14
6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} 15 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
7 knitr::opts_chunk$set(error = TRUE) 16 knitr::opts_chunk$set(error = TRUE)
8 ``` 17 ```
9 18
14 23
15 # build script file: script.sh 24 # build script file: script.sh
16 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 25 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
17 sep = '|', header = TRUE) 26 sep = '|', header = TRUE)
18 27
28 # prepend A_TOOL_OUTPUT_PATH
29 if (nrow(df[df$type == 'path_relative_to_a_tool', ]) > 0) {
30 for (i in 1:nrow(df[df$type == 'path_relative_to_a_tool', ])) {
31 root_path = readLines(df[df$type == 'path_relative_to_a_tool', ][i, 'path_type'])[1]
32 df[df$type == 'path_relative_to_a_tool', ][i, 'value'] = paste(root_path,
33 df[df$type == 'path_relative_to_a_tool', ][i, 'value'],
34 sep = '/')
35 }
36 }
37
19 # get tool name 38 # get tool name
20 tool_name = df[df$type == 'tool_name', 'value'] 39 tool_name = df[df$type == 'tool_name', 'value']
21 # build script for displaying help messages (this probably should be tool specific) 40 # build script for displaying help messages (this probably should be tool specific)
22 write(paste0(tool_name, ' -h'), 41 write(paste0(tool_name, ' -h'),
23 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh')) 42 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh'))
24 43
25 knitr::kable(df[, c('flag', 'value')]) 44 knitr::kable(df)
26 45
27 # if the number of option/argument pairs is larger than 0, build script file 46 # if the number of option/argument pairs is larger than 0, build script file
28 df2 = df[df$type != 'tool_name', ] 47 df2 = df[df$type != 'tool_name', ]
29 if (nrow(df2) > 0) { 48 if (nrow(df2) > 0) {
30 # write tool name as the first line of the script.sh 49 # write tool name as the first line of the script.sh
54 ```{bash, echo=FALSE} 73 ```{bash, echo=FALSE}
55 ## code to open help documentation 74 ## code to open help documentation
56 sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC} 75 sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC}
57 ``` 76 ```
58 77
59 ```{bash, results='asis', echo=FALSE} 78
60 echo '## Show help documentation' 79 ```{r, echo=FALSE}
61 echo '' 80 # create paths before running the job script
62 echo '' 81 df_paths = df[df$type == 'path_relative_to_this_tool', ]
63 echo '```bash' 82
64 cat ${REPORT_FILES_PATH}/help.sh 83 if (nrow(df_paths) > 0) {
65 echo '```' 84 for (i in 1:nrow(df_paths)) {
85 path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/', df_paths[i, 'value'])
86 path_type = df_paths[i, 'path_type']
87
88 # create file paths
89 if ((path_type == 'file_path') & !file.exists(path)) {
90 dir_path = paste(head(strsplit(path, '/')[[1]], -1), collapse = '/' )
91 if (!dir.exists(dir_path)) {
92 dir.create(dir_path, recursive = TRUE)
93 }
94 file.create(path)
95 }
96
97 # create dir paths
98 if ((path_type == 'dir_path') & !dir.exists(path)) {
99 dir.create(path, recursive = TRUE)
100 }
101 }
102 }
66 ``` 103 ```
67 104
68 105
69 ```{bash, echo=FALSE} 106 ```{bash, echo=FALSE}
70 # run job script 107 # run job script
71 # it's important to run the job within the REPORT_FILES_PATH 108 # it's important to run the job within the REPORT_FILES_PATH
72 cd ${REPORT_FILES_PATH} && sh script.sh 109 cd ${REPORT_FILES_PATH} && sh script.sh
73 ``` 110 ```
74 111
112
113
75 ```{bash, results='asis', echo=FALSE} 114 ```{bash, results='asis', echo=FALSE}
76 echo '## Job script' 115 echo '## Job script'
77 echo '' 116 echo ''
78 echo '' 117 echo ''
79 echo '```bash' 118 echo '```bash'
80 cat ${REPORT_FILES_PATH}/script.sh 119 cat ${REPORT_FILES_PATH}/script.sh
81 echo '```' 120 echo '```'
121 ```
122
123
124 ```{r, echo=FALSE}
125 ## obtain REPORT_FILES_PAHT and save it to a galaxy output.
126 database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
127 tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
128 tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
129 write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
82 ``` 130 ```
83 131
84 132
85 ```{r, results='asis', echo=FALSE} 133 ```{r, results='asis', echo=FALSE}
86 cat('##All output files') 134 cat('##All output files')