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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Tue, 12 Jun 2018 09:49:08 -0400
parents bd236d81187b
children c062782a7534
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1 ---
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2 title: 'Aurora Tool Report'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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7
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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10 ```
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11
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12 ```{css echo=FALSE}
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13 # code chunks scrollable
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14 pre code, pre, code {
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15 white-space: pre !important;
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16 overflow-x: scroll !important;
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17 word-break: keep-all !important;
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18 word-wrap: initial !important;
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19 }
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20 ```
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21
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23 ```{r, echo=FALSE}
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24 # to make the css theme to work, <link></link> tags cannot be added directly
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25 # as <script></script> tags as below.
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26 # it has to be added using a code chunk with the htmltool functions!!!
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27 css_link = tags$link()
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28 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
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29 css_link
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30 ```
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31
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32 ```{r, eval=FALSE, echo=FALSE}
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33 # this code chunk is purely for adding comments
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34 # below is to add jQuery and jstree javascripts
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35 ```
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36 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
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37 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
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39 ---
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40 # javascript code below is to build the file tree interface
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41 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
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42 ---
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43 <script>
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44 $(function () {
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45 // create an instance when the DOM is ready
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46 $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
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47 window.open( data.node.a_attr.href, data.node.a_attr.target )
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48 });
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49 });
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50 </script>
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51
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52 ---
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53 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
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54 ---
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55
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56 # Download and extract reads
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57
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58 ```{r echo=FALSE}
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59 # create two directories to store downloaded data
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60 se_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/se_read_files_dir')
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61 pe_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/pe_read_files_dir')
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62 ```
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63
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64 ```{r 'download and extract reads', echo=-1}
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65 Sys.setenv(PATH=paste0('/main/sites/galaxy/galaxy/tools/_conda/bin:', Sys.getenv('PATH')))
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66
0
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67 # download and extract reads (single end)
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68 sra_ids_se = strsplit(gsub(',', ' ', opt$X_s), ' ')[[1]]
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69 sra_ids_se = sra_ids_se[sra_ids_se != '']
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70 # loop through SRA accessions to download and extract reads.
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71 for(id in sra_ids_se) {
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72 # build URL from SRA id
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73 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
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74 substr(id, 1, 3), '/',
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75 substr(id, 1, 6), '/', id, '/', id, '.sra')
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76 # download sra file with bdss
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77 bdss_command = paste0('bdss transfer -u ', url)
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78 command_stdout = system(bdss_command, intern = TRUE)
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79 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE)
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80 # convert .sra to .fastq/.fasta
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81 if(opt$X_f == 'fasta') {
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82 command = paste0('fastq-dump --fasta -O se_read_files_dir ', id, '.sra')
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83 } else {
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84 command = paste0('fastq-dump -O se_read_files_dir ', id, '.sra')
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85 }
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86 cat('----convert SRA to fastq/fasta------\n')
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87 command_stdout = system(command, intern = TRUE)
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88 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
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89 }
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90
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91 # download and extract reads (paired end)
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92 sra_ids_pe = strsplit(gsub(',', ' ', opt$X_p), ' ')[[1]]
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93 sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
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94 # loop through SRA accessions to download and extract reads.
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95 for(id in sra_ids_pe) {
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96 # build URL from SRA id
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97 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
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98 substr(id, 1, 3), '/',
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99 substr(id, 1, 6), '/', id, '/', id, '.sra')
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100 # download sra file with bdss
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101 bdss_command = paste0('bdss transfer -u ', url)
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102 command_stdout = system(bdss_command, intern = TRUE)
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103 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE)
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104 # convert .sra to .fastq/.fasta
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105 if(opt$X_f == 'fasta') {
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106 command = paste0('fastq-dump --fasta --split-files -O pe_read_files_dir ', id, '.sra')
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107 } else {
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108 command = paste0('fastq-dump --split-files -O pe_read_files_dir ', id, '.sra')
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109 }
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110 cat('----convert SRA to fastq/fasta------\n')
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111 command_stdout = system(command, intern = TRUE)
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112 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
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113 if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) {
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114 # this is not a paired end SRA file. The corresponding file will be deleted.
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115 cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
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116 command_stdout = system(paste0('rm pe_read_files_dir/', id, '_1.*'), intern = TRUE)
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117 }
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118
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119 }
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120
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121
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122 cat('-----Renaming files------\n')
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123 # rename files for paired end reads
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124 old_files = paste0('./pe_read_files_dir/', list.files('./pe_read_files_dir'))
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125 new_files = gsub('_1', '_forward', old_files)
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126 new_files = gsub('_2', '_reverse', new_files)
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127 file.rename(old_files, new_files)
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128 ```