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comparison abims_sartools_edger_wrapper.py @ 0:581d217c7337 draft

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Planemo upload
author lgueguen
date Fri, 22 Jul 2016 05:39:13 -0400
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children de6d0b7c17af
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-1:000000000000 0:581d217c7337
1 #abims_sartools_edger_wrapper.py
2 #Author: Loraine Gueguen
3 # imports
4 import os, argparse
5
6
7
8 def main():
9
10 print("Start of galaxy wrapper")
11
12 #Check R and Rscript are installed
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; }"
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; }"
15 os.system(check_r_cmd)
16 os.system(check_rscript_cmd)
17
18 #Get arguments
19 parser = argparse.ArgumentParser()
20 parser.add_argument('--projectName')
21 parser.add_argument('--author')
22 parser.add_argument('--targetFile')
23 parser.add_argument('--rawDir')
24 parser.add_argument('--featuresToRemove')
25 parser.add_argument('--varInt')
26 parser.add_argument('--condRef')
27 parser.add_argument('--batch')
28 parser.add_argument('--alpha')
29 parser.add_argument('--pAdjustMethod')
30 parser.add_argument('--cpmCutoff')
31 parser.add_argument('--geneSelection')
32 parser.add_argument('--normalizationMethod')
33 parser.add_argument('--colors')
34 parser.add_argument('--figures_html')
35 parser.add_argument('--figures_html_files_path')
36 parser.add_argument('--tables_html')
37 parser.add_argument('--tables_html_files_path')
38 parser.add_argument('--rdata')
39 parser.add_argument('--report_html')
40 parser.add_argument('--log')
41 args = parser.parse_args()
42 projectName=args.projectName
43 author=args.author
44 targetFile=args.targetFile
45 rawDir=args.rawDir
46 featuresToRemove=args.featuresToRemove
47 varInt=args.varInt
48 condRef=args.condRef
49 batch=args.batch
50 alpha=args.alpha
51 pAdjustMethod=args.pAdjustMethod
52 cpmCutoff=args.cpmCutoff
53 geneSelection=args.geneSelection
54 normalizationMethod=args.normalizationMethod
55 colors=args.colors
56 figures_html=args.figures_html
57 figures_html_files_path=args.figures_html_files_path
58 tables_html=args.tables_html
59 tables_html_files_path=args.tables_html_files_path
60 rdata=args.rdata
61 report_html=args.report_html
62 log=args.log
63 #Print the parameters selected
64 print("Wrapper arguments: %s") %(args)
65
66 #Get the working directory path
67 working_directory = os.getcwd()
68 #Get the script directory path
69 script_directory=os.path.dirname(os.path.realpath(__file__))
70
71 #Unzip files from rawDir
72 rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
73 os.mkdir(rawDir_unzipped_path)
74 unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
75 os.system(unzip_cmd)
76
77 #Create the command
78 cmd="Rscript --no-save --no-restore %s/template_script_edgeR_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
79 cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
80 if batch and batch!="NULL":
81 cmd+="--batch %s " % (batch)
82 if alpha:
83 cmd+="--alpha %s " % (alpha)
84 if pAdjustMethod:
85 cmd+="--pAdjustMethod %s " % (pAdjustMethod)
86 if cpmCutoff:
87 cmd+="--cpmCutoff %s " % (cpmCutoff)
88 if geneSelection:
89 cmd+="--gene.selection %s " % (geneSelection)
90 if normalizationMethod:
91 cmd+="--normalizationMethod %s " % (normalizationMethod)
92 if colors:
93 cmd+="--colors %s " % (colors)
94 cmd+="> %s 2>&1" % (log)
95 print("Rscript command: %s") % (cmd)
96 os.system(cmd)
97
98 #Get output files
99 os.mkdir(figures_html_files_path)
100 os.mkdir(tables_html_files_path)
101 rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
102 rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
103 os.system(rsync_figures_dir_cmd)
104 os.system(rsync_tables_dir_cmd)
105 figures_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Figures --output_dir %s --output_html %s" % (script_directory,figures_html_files_path,figures_html)
106 tables_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Tables --output_dir %s --output_html %s" % (script_directory,tables_html_files_path,tables_html)
107 os.system(figures_html_create_cmd)
108 os.system(tables_html_create_cmd)
109 rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
110 rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
111 os.system(rsync_rdata_file_cmd)
112 os.system(rsync_report_file_cmd)
113
114 print("End of galaxy wrapper")
115
116 if __name__ == '__main__':
117 main()
118
119