Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

annotate i_adhore_configure.Rmd @ 1:fd719a0a6b26 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author mingchen0919
date Tue, 08 Aug 2017 12:59:51 -0400
parents 9755ce6ac4d5
children dab02b629d48
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mingchen0919
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1 ---
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2 title: 'i-adhore: generate i-adhore config file'
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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$set(echo = ECHO)
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13 ```
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15 # Genomes and analysis files
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17 ```{r}
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18 g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]]
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19 g_analysis_files_list = list()
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20 # for(i in g_analysis_files_set) {
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21 # genome = strsplit(i, ':')[[1]][1]
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22 # analysis_files = strsplit(i, ':')[[1]][2] %>%
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23 # strsplit(',') %>% `[[`(1) %>%
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24 # (function(x){
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25 # paste0(1:length(x),' ', x)
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26 # })
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27 # g_analysis_files_list[[genome]] = analysis_files
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28 # }
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29 for(i in g_analysis_files_set) {
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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30 genome = strsplit(i, ':')[[1]][1]
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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31 analysis_files = strsplit(i, ':')[[1]][2] %>%
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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32 strsplit(',') %>% `[[`(1) %>%
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33 laply(.fun = function(x){
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34 file_name = strsplit(x, '/')[[1]] %>% tail(1)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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35 file_name = strsplit(file_name, '\\.')[[1]][1]
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36 paste0(file_name, ' ', x)
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37 })
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38 g_analysis_files_list[[genome]] = c(
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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39 'name' = paste0('genome=', strsplit(i, ':')[[1]][1]),
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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40 'analysis_files' = analysis_files
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41 )
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42 print(paste0('genome=', strsplit(i, ':')[[1]][1]))
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43 print(analysis_files)
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44 }
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45 ```
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46
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47 # Other parameters
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48
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49 ```{r}
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50 params = c(
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51 'blast table' = opt$blast_table,
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52 'output_path' = opt$i_adhore_configure_dir,
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53 'gap_size' = opt$gap_size,
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54 'cluster_gap' = opt$cluster_gap,
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55 'q_value' = opt$q_value,
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56 'prob_cutoff' = opt$prob_cutoff,
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57 'anchor_points' = opt$anchor_points,
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58 'level_2_only' = opt$level2only,
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59 'table_type' = opt$table_type,
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60 'multi_hypothesis_correction' = opt$multi_hypothesis_correction
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61 )
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62
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63 df = data.frame(name = names(params),
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64 value = params)
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65 knitr::kable(df)
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66 ```
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68
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69 ```{r echo=FALSE}
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70 # generate i_adhore_configure.txt file
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71 lines = c(unlist(g_analysis_files_list),
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72 ' ',
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73 paste0(df$name, '=', df$value),
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74 'CompareAligners')
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75 fileConn = file('I_ADHORE_CONFIGURE_TXT')
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76 writeLines(lines, con = fileConn)
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77 ```
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