# HG changeset patch
# User stevecassidy
# Date 1511236272 18000
# Node ID 278da6e5ab117426f98382f5b2d74b31f1aeff24
# Parent  fe887de9b4b51f258c048beefe3f777bb8574d3f
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2

diff -r fe887de9b4b5 -r 278da6e5ab11 zipcollection.py
--- 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__':
diff -r fe887de9b4b5 -r 278da6e5ab11 zipcollection.xml
--- a/zipcollection.xml	Thu Nov 16 06:19:53 2017 -0500
+++ b/zipcollection.xml	Mon Nov 20 22:51:12 2017 -0500
@@ -2,12 +2,19 @@
     <description>from one or more datasets</description>
 
     <command interpreter="python">
-        zipcollection.py --dataset "${",".join(map(str, $dataset))}"  --identifier "${",".join(map(str, [t.element_identifier + "." + t.extension for t in $dataset]))}" --output $output
+        zipcollection.py --dataset "${",".join(map(str, $dataset))}"
+        --identifier "${",".join(map(str, [t.element_identifier + "." + t.extension for t in $dataset]))}"
+        #if $extension:
+          --extension $extension
+        #end if
+        --output $output
     </command>
 
     <inputs>
         <param name="dataset" format="data" type="data"
                multiple="true" label="DataSets" help="Datasets to include in zip"/>
+        <param name="extension" type="text" size="10" format="text"
+               label="New extension for files (leave empty to use the dataset type, eg txt, tabbed)"/>
         <param name="job_name" type="text" size="25"
                label="Name of output zip file" value="dataset"/>
     </inputs>
@@ -21,9 +28,9 @@
         <test>
             <param name="dataset" value="textgrids/1_1308_2_22_020-ch6-speaker16.TextGrid_TextGrid"/>
             <param name="job_name" value="test.zip"/>
-            <output name="output" ftype="zip"/>
+            <output name="output" ftype="zip" file="test.zip"/>
         </test>
-        -->
+         -->
     </tests>
 
     <help>Creates a zip file from a dataset or dataset collection</help>