Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

comparison i_adhore_configure.Rmd @ 13:d41a3115e470 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 377565cfe72b3455320ea04b7c58191bf4428d79-dirty
author mingchen0919
date Tue, 29 Aug 2017 21:48:28 -0400
parents fcd72af3f41e
children e10d998b078d
comparison
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12:fcd72af3f41e 13:d41a3115e470
10 10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} 11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(echo = ECHO) 12 knitr::opts_chunk$set(echo = ECHO)
13 ``` 13 ```
14 14
15 ```{r echo=FALSE}
15 # Genomes and analysis files 16 # Genomes and analysis files
16
17 ```{r}
18 g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]] 17 g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]]
19 g_analysis_files_list = list() 18 g_analysis_files_list = list()
20 # for(i in g_analysis_files_set) {
21 # genome = strsplit(i, ':')[[1]][1]
22 # analysis_files = strsplit(i, ':')[[1]][2] %>%
23 # strsplit(',') %>% `[[`(1) %>%
24 # (function(x){
25 # paste0(1:length(x),' ', x)
26 # })
27 # g_analysis_files_list[[genome]] = analysis_files
28 # }
29 for(i in g_analysis_files_set) { 19 for(i in g_analysis_files_set) {
30 genome = strsplit(i, ':')[[1]][1] 20 genome = strsplit(i, ':')[[1]][1]
31 analysis_files = strsplit(i, ':')[[1]][2] %>% 21 analysis_files = strsplit(i, ':')[[1]][2] %>%
32 strsplit(',') %>% `[[`(1) %>% 22 strsplit(',') %>% `[[`(1) %>%
33 laply(.fun = function(x){ 23 laply(.fun = function(x){
37 }) 27 })
38 g_analysis_files_list[[genome]] = c( 28 g_analysis_files_list[[genome]] = c(
39 'name' = paste0('genome=', strsplit(i, ':')[[1]][1]), 29 'name' = paste0('genome=', strsplit(i, ':')[[1]][1]),
40 'analysis_files' = analysis_files 30 'analysis_files' = analysis_files
41 ) 31 )
42 print(paste0('genome=', strsplit(i, ':')[[1]][1])) 32 #print(paste0('genome=', strsplit(i, ':')[[1]][1]))
43 print(analysis_files) 33 #print(analysis_files)
44 } 34 }
45 ``` 35 ```
46 36
47 # Other parameters 37 # Tool parameters
48 38
49 ```{r} 39 ```{r}
50 output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1) 40 output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1)
51 output_path = gsub('dataset_.*dat', output_dir, opt$blast_table) 41 output_path = gsub('dataset_.*dat', output_dir, opt$blast_table)
52 42
83 73
84 # I-ADHoRe analysis results 74 # I-ADHoRe analysis results
85 75
86 ```{bash} 76 ```{bash}
87 # run i-adhore analysis 77 # run i-adhore analysis
88 i-adhore I_ADHORE_CONFIGURE_TXT 78 i-adhore I_ADHORE_CONFIGURE_TXT > /dev/null 2>&1
89 ``` 79 ```
90 80
91 Links to outputs 81 Links to outputs
92 82
93 ```{r} 83 ```{r}