diff refinery_file_splitter.py @ 1:b87749d7a24c draft default tip

planemo upload commit 4fb0a789956149e5a58f4e370d7fe14f4e8bcf79

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/refinery_file_splitter.py	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+'''
+Test tool for splitting output files from Refinery Test Tools
+
+@author: Scott Ouellette
+
+Input: one text file
+Output: N output files based on the amount of input files that 
+got concatenated from Refinery test tool runs
+
+Requires Python v2.7
+
+'''
+
+import re
+import argparse
+
+
+def main(args):
+    create_many_files(args.input_file)
+
+
+def create_many_files(input_file):
+    # Split file's content when we see data that wasn't added by test tool runs
+    file_content = re.split("Output.*|Input.*", input_file.read())
+
+    sanitized_data = [
+        data.lstrip("\n") for data in file_content if data.rstrip("\n")]
+
+    # Create N ouput files based on the number of inputs run through test tools
+    for num, file_content in enumerate(sanitized_data):
+        open("Output file {}.txt".format(num + 1), 'w').write(file_content)
+
+
+if __name__ == '__main__':
+    version = "%(prog)s 0.1"
+    description = "Test tool for running workflows on Galaxy platform from Refinery"
+    parser = argparse.ArgumentParser(description=description, version=version)
+
+    parser.add_argument('-i', '--in-file', dest='input_file',
+                        type=file, metavar='INPUT_FILE', required=True,
+                        help='name of the input file')
+
+    # check argument values for errors
+    try:
+        args = parser.parse_args()
+    except IOError as e:
+        parser.error(e)
+
+    main(args)