--- a/nested_collection.xml	Sat Apr 08 08:23:12 2017 -0400
+++ b/nested_collection.xml	Fri Apr 28 12:25:36 2017 -0400
@@ -38,37 +38,51 @@
     <outputs>
         <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
           <filter>filetype == "mzid"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="mzid" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="mzid" visible="false" />
         </collection>
         <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
           <filter>filetype == "percout"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="percout" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="percout" visible="false" />
         </collection>
         <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
           <filter>filetype == "tabular"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="tabular" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="tabular" visible="false" />
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name="batchsize" value="2"/>
+            <param name="batchsize" value="6"/>
             <param name="filetype" value="mzid" />
             <param name="listtobatch">
                 <collection type="list">
-                    <element name="fraction_one_spectra" value="empty_file1.mzid"/>
+                    <element name="fraction_one_spectra.mzML" value="empty_file1.mzid"/>
                     <element name="fraction_two_spectra" value="empty_file2.mzid"/>
                     <element name="fraction_three_spectra" value="empty_file3.mzid"/>
                     <element name="fraction_four_spectra" value="empty_file4.mzid"/>
+                    <element name="fraction_five_spectra" value="empty_file5.mzid"/>
+                    <element name="fraction_six_spectra" value="empty_file6.mzid"/>
+                    <element name="fraction_seven_spectra" value="empty_file7.mzid"/>
+                    <element name="fraction_eight_spectra" value="empty_file8.mzid"/>
+                    <element name="fraction_nine_spectra" value="empty_file9.mzid"/>
+                    <element name="fraction_ten_spectra" value="empty_file10.mzid"/>
+                    <element name="fraction_eleven_spectra" value="empty_file11.mzid"/>
                 </collection>
             </param>
             <output_collection name="batched_fractions_mzid" type="list:list">
                 <element name="pool0_batch0">
-                    <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/>
-                    <element name="inputfn1" ftype="mzid" file="empty_file2.mzid"/>
+                    <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/>
+                    <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/>
+                    <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/>
+                    <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/>
+                    <element name="inputfn04_fraction_five_spectra" ftype="mzid" file="empty_file5.mzid"/>
+                    <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/>
                 </element>
                 <element name="pool0_batch1">
-                    <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/>
-                    <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/>
+                    <element name="inputfn06_fraction_seven_spectra" ftype="mzid" file="empty_file7.mzid"/>
+                    <element name="inputfn07_fraction_eight_spectra" ftype="mzid" file="empty_file8.mzid"/>
+                    <element name="inputfn08_fraction_nine_spectra" ftype="mzid" file="empty_file9.mzid"/>
+                    <element name="inputfn09_fraction_ten_spectra" ftype="mzid" file="empty_file10.mzid"/>
+                    <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file10.mzid"/>
                 </element>
             </output_collection>
         </test>
@@ -85,21 +99,37 @@
                     <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
                     <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
                     <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
-                    <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
-                    <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
-                    <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
+                    <element name="fr_four_set1_spectra" value="empty_file4.mzid"/>
+                    <element name="fr_five_set1_spectra" value="empty_file5.mzid"/>
+                    <element name="fr_six_set1_spectra" value="empty_file6.mzid"/>
+                    <element name="fr_seven_set1_spectra" value="empty_file7.mzid"/>
+                    <element name="fr_eight_set1_spectra" value="empty_file8.mzid"/>
+                    <element name="fr_nine_set1_spectra" value="empty_file9.mzid"/>
+                    <element name="fr_ten_set1_spectra" value="empty_file10.mzid"/>
+                    <element name="fr_eleven_set1_spectra" value="empty_file11.mzid"/>
+                    <element name="fr_one_set2_spectra" value="empty_file12.mzid"/>
+                    <element name="fr_two_set2_spectra" value="empty_file13.mzid"/>
+                    <element name="fr_three_set2_spectra" value="empty_file14.mzid"/>
                 </collection>
             </param>
             <output_collection name="batched_fractions_tab" type="list:list">
                 <element name="set1_batch0">
-                    <element name="inputfn0" ftype="tabular" file="empty_file1.mzid"/>
-                    <element name="inputfn1" ftype="tabular" file="empty_file2.mzid"/>
-                    <element name="inputfn2" ftype="tabular" file="empty_file3.mzid"/>
+                    <element name="inputfn00_fr_one_set1_spectra" ftype="tabular" file="empty_file1.mzid"/>
+                    <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/>
+                    <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/>
+                    <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/>
+                    <element name="inputfn04_fr_five_set1_spectra" ftype="tabular" file="empty_file5.mzid"/>
+                    <element name="inputfn05_fr_six_set1_spectra" ftype="tabular" file="empty_file6.mzid"/>
+                    <element name="inputfn06_fr_seven_set1_spectra" ftype="tabular" file="empty_file7.mzid"/>
+                    <element name="inputfn07_fr_eight_set1_spectra" ftype="tabular" file="empty_file8.mzid"/>
+                    <element name="inputfn08_fr_nine_set1_spectra" ftype="tabular" file="empty_file9.mzid"/>
+                    <element name="inputfn09_fr_ten_set1_spectra" ftype="tabular" file="empty_file10.mzid"/>
+                    <element name="inputfn10_fr_eleven_set1_spectra" ftype="tabular" file="empty_file11.mzid"/>
                 </element>
                 <element name="set2_batch1">
-                    <element name="inputfn0" ftype="tabular" file="empty_file4.mzid"/>
-                    <element name="inputfn1" ftype="tabular" file="empty_file5.mzid"/>
-                    <element name="inputfn2" ftype="tabular" file="empty_file6.mzid"/>
+                    <element name="inputfn0_fr_one_set2_spectra" ftype="tabular" file="empty_file12.mzid"/>
+                    <element name="inputfn1_fr_two_set2_spectra" ftype="tabular" file="empty_file13.mzid"/>
+                    <element name="inputfn2_fr_three_set2_spectra" ftype="tabular" file="empty_file14.mzid"/>
                 </element>
             </output_collection>
         </test>
@@ -124,18 +154,18 @@
             </param>
             <output_collection name="batched_fractions_perco" type="list:list">
                 <element name="set1_batch0">
-                    <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/>
-                    <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/>
+                    <element name="inputfn0_fr_one_set1_spectra" ftype="percout" file="empty_file1.mzid"/>
+                    <element name="inputfn1_fr_two_set1_spectra" ftype="percout" file="empty_file2.mzid"/>
                 </element>
                 <element name="set1_batch1">
-                    <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/>
+                    <element name="inputfn2_fr_three_set1_spectra" ftype="percout" file="empty_file3.mzid"/>
                 </element>
                 <element name="set2_batch2">
-                    <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/>
-                    <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/>
+                    <element name="inputfn0_fr_one_set2_spectra" ftype="percout" file="empty_file4.mzid"/>
+                    <element name="inputfn1_fr_two_set2_spectra" ftype="percout" file="empty_file5.mzid"/>
                 </element>
                 <element name="set2_batch3">
-                    <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/>
+                    <element name="inputfn2_fr_three_set2_spectra" ftype="percout" file="empty_file6.mzid"/>
                 </element>
             </output_collection>
         </test>