--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Test_input_into_file.py	Tue Nov 27 14:20:40 2018 -0500
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+#Created on Jule 23, 2018
+
+# @author: Bob Brown 
+
+import sys
+import os
+
+def main():
+
+    # Grab the inputs from the Galaxy xml interface and write to a file that is passed to the program
+    # Not each of the  parameters as separate command line variables.
+#    ab_gene_name_for_header={}
+#    ab_rrid_for_header={}
+    dir= "/Users/bobbrown/Desktop/junk/"
+    accepted_extensions = ["csv", "tsv"]
+    filenames = [fn for fn in os.listdir(dir) if fn.split(".")[-1] in accepted_extensions]    
+    for f in filenames:
+        print("filename= "+f)
+        os.remove(dir+f)
+        
+    sys.exit(0)
+    
+    ab_gene_name_for_header={'abc':'geneName'}
+    ab_rrid_for_header={'abc':'rrid123'}
+    line=  'abc,123\n'
+    
+    pos= line.find(",")
+    ABname= line[0:pos]
+    ABnewName= ABname+ "|"+ab_gene_name_for_header[ABname]+"|"+ab_rrid_for_header[ABname]    
+    line= ABnewName+line[pos:]
+    line= line.replace(',','\t')
+    sys.exit(0)
+#    try:
+    print(' \n starting Test program read params from file stored in tools dir. Arguments=')
+    print(str(sys.argv[1:])+'\n')
+                
+    if False:
+        infileName    = sys.argv[1]
+    #    directory     = sys.argv[2]
+        directory     = '/Users/bobbrown/Desktop/'
+        outfileName   = sys.argv[3]   #use later
+    #        outfile      = sys.argv[6]
+        
+    #sys.stdout.write
+    
+     #   ifile= open(directory+"/"+infileName,'rU')
+        ifile= open(directory+infileName,'rU')
+        ofile= open(directory+outfileName,'w')
+    #    ofile= open('/Users/bobbrown/Desktop/TestOutFileVarParams.txt','w')
+    
+        cnt= 0
+    #     for param in range(2,len(sys.argv)):
+    #         cnt +=1
+    #         ofile.write("param "+str(cnt)+"= "+param+"\n")
+    
+    
+        for param in ifile:
+            cnt +=1
+            ofile.write("param "+str(cnt)+"= "+param)
+     
+        ifile.close()
+    
+        ofile.close()
+    
+        print('Fini -- rows read = '+str(cnt)+'\n')        
+
+#    except :
+#        print('Error>>> ')
+
+    return
+##
+##
+
+if __name__ == '__main__': main()
+    #sys.exit(0)
\ No newline at end of file