--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kisspliceGWrapper.py	Fri Jun 05 11:40:36 2015 -0400
@@ -0,0 +1,75 @@
+import subprocess, os, sys, shutil, tempfile, os.path
+from os.path import basename, splitext
+
+## inputs
+kmer_value = sys.argv[7]
+smallc_value = sys.argv[8]
+bigc_value = sys.argv[9]
+output_contex_value = sys.argv[10]
+counts_value = sys.argv[11]
+input_dat = sys.argv[12:len(sys.argv):2] # contains filename1... filenameq
+input_ext = sys.argv[13:len(sys.argv):2] # contains extension1... extensionq
+
+## tmp directory
+tmp_dir = tempfile.mkdtemp(prefix='kissplice-galaxy.')
+
+## command line (init)
+command_line = []
+command_line.append("kissplice")
+
+## symlink for .fasta/q (extension required)
+## command line built with -r option
+identifier = ""
+for i in range(0,len(input_dat)):
+	tmp_input_fasta =  os.path.join(tmp_dir, 'input'+str(i)+'.'+input_ext[i])
+	identifier += 'input'+str(i)+'_'
+	os.symlink(input_dat[i], tmp_input_fasta)
+	command_line.append("-r")
+	command_line.append(tmp_input_fasta)
+
+## command line (end)
+opath=tmp_dir+"/results"
+nocontext = ""
+nosnp = ""
+if output_contex_value == "yes":
+	command_line.extend(["-k", kmer_value, 
+			     "-c", smallc_value, "-C", bigc_value,
+			     "--counts", counts_value, "--output-context",
+			     "-o", opath, "-s"])
+else:
+	command_line.extend(["-k", kmer_value, 
+			     "-c", smallc_value, "-C", bigc_value,
+			     "--counts", counts_value,
+			     "-o", opath, "-s"])
+
+## running kissplice
+p=subprocess.Popen(command_line, 
+		   stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+stdoutput = p.communicate()
+
+## outputs
+output_f1=sys.argv[1]
+out1=open(output_f1, 'w' )
+out1.write(stdoutput[0])
+out1.close()
+
+output_type0=sys.argv[2]
+output_type1=sys.argv[3]
+output_type2=sys.argv[4]
+output_type3=sys.argv[5]
+output_type4=sys.argv[6]
+
+result_type0 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_0.fa"
+result_type1 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_1.fa"
+result_type2 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_2.fa"
+result_type3 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_3.fa"
+result_type4 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_4.fa"
+
+shutil.move(result_type0, output_type0)
+shutil.move(result_type1, output_type1)
+shutil.move(result_type2, output_type2)
+shutil.move(result_type3, output_type3)
+shutil.move(result_type4, output_type4)
+
+## cleaning
+shutil.rmtree(tmp_dir)