diff run_seqsero.py @ 3:38ad1130d077 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- a/run_seqsero.py	Sun Nov 12 02:27:32 2017 -0500
+++ b/run_seqsero.py	Mon Nov 27 11:21:07 2017 -0500
@@ -4,13 +4,23 @@
 import subprocess
 from subprocess import Popen, PIPE
 
-database = '/nfs/sw/apps/galaxy/database/universe.sqlite'
-seqsero = '/nfs/sw/apps/galaxy/tools/seqsero/SeqSero.py'
-test_out = open("/nfs/sw/apps/galaxy/tools/seqsero/test.txt", 'w')
-out_path = '/nfs/sw/apps/galaxy/database/files/000'
-test_out2 = open("/nfs/sw/apps/galaxy/tools/seqsero/test2.txt", 'w')
+
+# Declare Variables 
+# paths to files and scripts
+
+fileDir = os.path.dirname(os.path.realpath('__file__'))
+print fileDir
 
-path2sample = '/nfs/sw/apps/galaxy/tools/seqsero/fastq_tmp'
+fq_list1 = []
+Tool_directory  = sys.argv[2]
+database = Tool_directory + '/universe.sqlite'
+seqsero = Tool_directory + 'SeqSero.py'
+test_out = open(Tool_directory + "/test.txt", 'w')
+out_path = Tool_directory + '/files/000'
+test_out2 = open(Tool_directory + "/test2.txt", 'w')
+
+path2sample = Tool_directory + 'fastq_tmp'
+
 
 #test_out2.write(" Test test test");
 
@@ -18,8 +28,10 @@
 #test_out.write("");
 test_out.write("\t".join(sys.argv)+'\n')
 
-fq_list1 = []
-fq_list2 = []
+
+
+
+print Tool_directory + '  path printed '
 
 test_out.write(str(len(sys.argv))+"\n")
 if len(sys.argv) >= 2:
@@ -33,7 +45,7 @@
 def print_time():
         test_out.write(time.asctime( time.localtime(time.time())))
 
-tmp_path = "/nfs/sw/apps/galaxy/tools/seqsero/fastq_tmp"
+tmp_path = "fastq_tmp"
 if not os.path.exists(tmp_path):
         os.system('mkdir '+tmp_path)
 
@@ -188,6 +200,13 @@
         html_out.write('</html>\n')
         html_out.close()
 
+
+def readFile(filename):
+    filehandle = open(filename)
+    print filehandle.read()
+    filehandle.close()
+
+
 run2fastqs = list_runs(fastq_files)
 outputs = run_seqsero(run2fastqs)
 fastq2serotype, fastq2comment = get_serotypes(outputs)