--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_sartools_deseq2_wrapper.py	Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,127 @@
+#abims_sartools_deseq2_wrapper.py
+#Author: Loraine Gueguen
+# imports
+import os, argparse
+
+
+
+def main():
+
+    print("Start of galaxy wrapper")
+
+    #Check R and Rscript are installed
+    check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed.  Aborting.'; exit 1; }"
+    check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed.  Aborting.'; exit 1; }"
+    os.system(check_r_cmd)
+    os.system(check_rscript_cmd)
+
+    #Get arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--projectName')
+    parser.add_argument('--author')
+    parser.add_argument('--targetFile')
+    parser.add_argument('--rawDir')
+    parser.add_argument('--featuresToRemove')
+    parser.add_argument('--varInt')
+    parser.add_argument('--condRef')
+    parser.add_argument('--batch')
+    parser.add_argument('--fitType')
+    parser.add_argument('--cooksCutoff')
+    parser.add_argument('--independentFiltering')
+    parser.add_argument('--alpha')
+    parser.add_argument('--pAdjustMethod')
+    parser.add_argument('--typeTrans')
+    parser.add_argument('--locfunc')
+    parser.add_argument('--colors')
+    parser.add_argument('--figures_html')
+    parser.add_argument('--figures_html_files_path')
+    parser.add_argument('--tables_html')
+    parser.add_argument('--tables_html_files_path')
+    parser.add_argument('--rdata')
+    parser.add_argument('--report_html')
+    parser.add_argument('--log')
+    args = parser.parse_args()
+    projectName=args.projectName
+    author=args.author
+    targetFile=args.targetFile
+    rawDir=args.rawDir
+    featuresToRemove=args.featuresToRemove
+    varInt=args.varInt
+    condRef=args.condRef
+    batch=args.batch
+    fitType=args.fitType
+    cooksCutoff=args.cooksCutoff
+    independentFiltering=args.independentFiltering
+    alpha=args.alpha
+    pAdjustMethod=args.pAdjustMethod
+    typeTrans=args.typeTrans
+    locfunc=args.locfunc
+    colors=args.colors
+    figures_html=args.figures_html
+    figures_html_files_path=args.figures_html_files_path
+    tables_html=args.tables_html
+    tables_html_files_path=args.tables_html_files_path
+    rdata=args.rdata
+    report_html=args.report_html
+    log=args.log
+    #Print the parameters selected
+    print("Wrapper arguments: %s") %(args)
+
+    #Get the working directory path
+    working_directory = os.getcwd()
+    #Get the script directory path
+    script_directory=os.path.dirname(os.path.realpath(__file__))
+ 
+    #Unzip files from rawDir
+    rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
+    os.mkdir(rawDir_unzipped_path)
+    unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
+    os.system(unzip_cmd)
+
+    #Create the command
+    cmd="Rscript --no-save --no-restore %s/template_script_DESeq2_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
+    cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
+    if batch and batch!="NULL":
+        cmd+="--batch %s " % (batch)
+    if fitType:
+        cmd+="--fitType %s " % (fitType)
+    if cooksCutoff:
+        cmd+="--cooksCutoff %s " % (cooksCutoff)
+    if independentFiltering:
+        cmd+="--independentFiltering %s " % (independentFiltering)
+    if alpha:
+        cmd+="--alpha %s " % (alpha)
+    if pAdjustMethod:
+        cmd+="--pAdjustMethod %s " % (pAdjustMethod)
+    if typeTrans:
+        cmd+="--typeTrans %s " % (typeTrans)
+    if locfunc:
+        cmd+="--locfunc %s " % (locfunc)
+    if colors:
+        cmd+="--colors %s " % (colors)
+    cmd+="> %s 2>&1" % (log)
+    print("Rscript command: %s") % (cmd)
+    os.system(cmd)
+
+    #Get output files
+    os.mkdir(figures_html_files_path)
+    os.mkdir(tables_html_files_path)
+    rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
+    rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
+    os.system(rsync_figures_dir_cmd)
+    os.system(rsync_tables_dir_cmd)
+    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)
+    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)
+    os.system(figures_html_create_cmd)
+    os.system(tables_html_create_cmd)
+    rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
+    rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
+    os.system(rsync_rdata_file_cmd)
+    os.system(rsync_report_file_cmd)
+
+    print("End of galaxy wrapper")
+
+if __name__ == '__main__':
+    main()
+
+