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1 #abims_sartools_deseq2_wrapper.py
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2 #Author: Loraine Gueguen
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3 # imports
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4 import os, argparse
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5
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6
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7
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8 def main():
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9
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10 print("Start of galaxy wrapper")
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11
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12 #Check R and Rscript are installed
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13 check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed. Aborting.'; exit 1; }"
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14 check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed. Aborting.'; exit 1; }"
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15 os.system(check_r_cmd)
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16 os.system(check_rscript_cmd)
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17
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18 #Get arguments
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--projectName')
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21 parser.add_argument('--author')
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22 parser.add_argument('--targetFile')
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23 parser.add_argument('--rawDir')
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24 parser.add_argument('--featuresToRemove')
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25 parser.add_argument('--varInt')
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26 parser.add_argument('--condRef')
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27 parser.add_argument('--batch')
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28 parser.add_argument('--fitType')
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29 parser.add_argument('--cooksCutoff')
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30 parser.add_argument('--independentFiltering')
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31 parser.add_argument('--alpha')
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32 parser.add_argument('--pAdjustMethod')
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33 parser.add_argument('--typeTrans')
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34 parser.add_argument('--locfunc')
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35 parser.add_argument('--colors')
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3
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36 parser.add_argument('--forceCairoGraph')
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0
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37 parser.add_argument('--figures_html')
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38 parser.add_argument('--figures_html_files_path')
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39 parser.add_argument('--tables_html')
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40 parser.add_argument('--tables_html_files_path')
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41 parser.add_argument('--rdata')
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42 parser.add_argument('--report_html')
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43 parser.add_argument('--log')
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44 args = parser.parse_args()
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45 projectName=args.projectName
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46 author=args.author
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47 targetFile=args.targetFile
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48 rawDir=args.rawDir
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49 featuresToRemove=args.featuresToRemove
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50 varInt=args.varInt
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51 condRef=args.condRef
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52 batch=args.batch
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53 fitType=args.fitType
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54 cooksCutoff=args.cooksCutoff
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55 independentFiltering=args.independentFiltering
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56 alpha=args.alpha
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57 pAdjustMethod=args.pAdjustMethod
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58 typeTrans=args.typeTrans
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59 locfunc=args.locfunc
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60 colors=args.colors
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3
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61 forceCairoGraph=args.forceCairoGraph
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0
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62 figures_html=args.figures_html
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63 figures_html_files_path=args.figures_html_files_path
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64 tables_html=args.tables_html
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65 tables_html_files_path=args.tables_html_files_path
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66 rdata=args.rdata
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67 report_html=args.report_html
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68 log=args.log
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69 #Print the parameters selected
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70 print("Wrapper arguments: %s") %(args)
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71
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72 #Get the working directory path
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73 working_directory = os.getcwd()
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74 #Get the script directory path
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75 script_directory=os.path.dirname(os.path.realpath(__file__))
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76
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77 #Unzip files from rawDir
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78 rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
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79 os.mkdir(rawDir_unzipped_path)
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80 unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
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81 os.system(unzip_cmd)
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82
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83 #Create the command
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84 cmd="Rscript --no-save --no-restore %s/template_script_DESeq2_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
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85 cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
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86 if batch and batch!="NULL":
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87 cmd+="--batch %s " % (batch)
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88 if fitType:
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89 cmd+="--fitType %s " % (fitType)
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90 if cooksCutoff:
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91 cmd+="--cooksCutoff %s " % (cooksCutoff)
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92 if independentFiltering:
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93 cmd+="--independentFiltering %s " % (independentFiltering)
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94 if alpha:
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95 cmd+="--alpha %s " % (alpha)
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96 if pAdjustMethod:
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97 cmd+="--pAdjustMethod %s " % (pAdjustMethod)
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98 if typeTrans:
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99 cmd+="--typeTrans %s " % (typeTrans)
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100 if locfunc:
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101 cmd+="--locfunc %s " % (locfunc)
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102 if colors:
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103 cmd+="--colors %s " % (colors)
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3
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104 if forceCairoGraph:
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105 cmd+="--forceCairoGraph %s " % (forceCairoGraph)
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0
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106 cmd+="> %s 2>&1" % (log)
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107 print("Rscript command: %s") % (cmd)
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108 os.system(cmd)
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109
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110 #Get output files
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111 os.mkdir(figures_html_files_path)
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112 os.mkdir(tables_html_files_path)
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113 rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
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114 rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
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115 os.system(rsync_figures_dir_cmd)
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116 os.system(rsync_tables_dir_cmd)
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117 figures_html_create_cmd="python %s/make_html.py --tool SARTools_DESeq2 --output_type Figures --output_dir %s --output_html %s" % (script_directory,figures_html_files_path,figures_html)
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118 tables_html_create_cmd="python %s/make_html.py --tool SARTools_DESeq2 --output_type Tables --output_dir %s --output_html %s" % (script_directory,tables_html_files_path,tables_html)
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119 os.system(figures_html_create_cmd)
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120 os.system(tables_html_create_cmd)
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121 rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
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122 rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
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123 os.system(rsync_rdata_file_cmd)
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124 os.system(rsync_report_file_cmd)
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125
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126 print("End of galaxy wrapper")
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127
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128 if __name__ == '__main__':
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129 main()
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130
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131
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