diff selection.py @ 5:af4f63f27c77 draft

planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selection.py	Wed Apr 08 15:34:17 2020 +0000
@@ -0,0 +1,38 @@
+import os
+import sys
+import subprocess
+import shutil
+
+def main():
+
+    input_file=sys.argv[1]
+    tmp_dir=sys.argv[4]
+    script_dir=os.path.dirname(os.path.abspath(__file__))
+    plot=sys.argv[11]
+    pdffigures=sys.argv[13]
+    outputlog=sys.argv[14]
+    log=sys.argv[15]
+    user=sys.argv[16]
+    package=sys.argv[17]
+        
+    iFile=open(input_file,'r')
+    dataSetLine=iFile.readline()
+    dataset=dataSetLine.split("\t")[1]
+    iFile.close()    
+        
+    if (outputlog=="TRUE"):
+        errfile=open(log,'w')
+    else:
+        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+    
+    retcode=subprocess.call(["Rscript", os.path.join(script_dir,"selection.R"), dataset, sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6], sys.argv[7], sys.argv[8], sys.argv[9], sys.argv[10], sys.argv[11], sys.argv[12],sys.argv[16],package], stdout = errfile, stderr = errfile)
+    
+    if (plot=="TRUE"):
+        shutil.copy(os.path.join(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures)
+    
+    errfile.close()
+       
+    sys.exit(retcode)
+
+if __name__ == "__main__":
+    main()