diff zipcollection.py @ 1:278da6e5ab11 draft default tip

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2

--- a/zipcollection.py	Thu Nov 16 06:19:53 2017 -0500
+++ b/zipcollection.py	Mon Nov 20 22:51:12 2017 -0500
@@ -1,11 +1,14 @@
 from __future__ import print_function
 import argparse
 from zipfile import ZipFile
+import os
+
 
 def parser():
     parser = argparse.ArgumentParser(description="Find matching segments in a TextGrid")
     parser.add_argument('--dataset', required=True, action="store", type=str, help="TextGrid files (comma separated)")
     parser.add_argument('--identifier', required=True, action="store", type=str, help="Dataset identifiers (comma separated)")
+    parser.add_argument('--extension', required=False, action='store', default='', type=str, help="Extension for stored files")
     parser.add_argument('--output', required=True, action="store", type=str, help="Path to output file")
     return parser.parse_args()
 
@@ -21,7 +24,15 @@
 
     with ZipFile(args.output, 'w') as zipfile:
         for dataset, identifier in pairs:
-            zipfile.write(dataset, identifier)
+
+            # rewrite extension if asked
+            if args.extension != '':
+                base, ext = os.path.splitext(identifier)
+                outname = base + "." + args.extension
+            else:
+                outname = identifier
+
+            zipfile.write(dataset, outname)
 
 
 if __name__ == '__main__':