# HG changeset patch
# User galaxyp
# Date 1491654192 14400
# Node ID abed51712ed0a889f72a2589f76ae70a1fdaa49c
# Parent  7a0951d0e13e7924418e357315cc6650abc2e20d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66

diff -r 7a0951d0e13e -r abed51712ed0 nested_collection.py
--- a/nested_collection.py	Fri Mar 10 03:20:52 2017 -0500
+++ b/nested_collection.py	Sat Apr 08 08:23:12 2017 -0400
@@ -44,7 +44,7 @@
     for batchcount, (pool_id, batch) in enumerate(get_batches_of_galaxyfiles(
             args.realnames, args.batchsize, args.poolids)):
         for fncount, batchfile in enumerate([args.galaxyfiles[index] for index in batch]):
-            dsetname = '{}_batch{}___inputfn{}.mzid'.format(pool_id, batchcount, fncount)
+            dsetname = '{}_batch{}___inputfn{}.data'.format(pool_id, batchcount, fncount)
             print('producing', dsetname)
             os.symlink(batchfile, dsetname)
 
diff -r 7a0951d0e13e -r abed51712ed0 nested_collection.xml
--- a/nested_collection.xml	Fri Mar 10 03:20:52 2017 -0500
+++ b/nested_collection.xml	Sat Apr 08 08:23:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="batched_set_list_creator" name="Create nested list" version="3.1">
+<tool id="batched_set_list_creator" name="Create nested list" version="3.2">
     <description>based on filenames and batch sizes</description>
     <stdio>
         <exit_code range="1:" />
@@ -24,6 +24,11 @@
     </command>
     <inputs>
         <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" />
+        <param name="filetype" type="select" label="Which datatype to nest?">
+            <option value="mzid">mzIdentML</option>
+            <option value="percout">Percolator out</option>
+            <option value="tabular">Tabular</option>
+        </param>
         <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)">
             <param name="pool_identifier" type="text" label="Filename part identifying batchpool" 
             help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/>
@@ -31,13 +36,23 @@
         <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
     </inputs>
     <outputs>
-        <collection name="batched_fractions" type="list:list" label="Pooled batched data">
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" />
+        <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" />
+        </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" />
+        </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" />
         </collection>
     </outputs>
     <tests>
         <test>
             <param name="batchsize" value="2"/>
+            <param name="filetype" value="mzid" />
             <param name="listtobatch">
                 <collection type="list">
                     <element name="fraction_one_spectra" value="empty_file1.mzid"/>
@@ -46,14 +61,14 @@
                     <element name="fraction_four_spectra" value="empty_file4.mzid"/>
                 </collection>
             </param>
-            <output_collection name="batched_fractions" type="list:list">
+            <output_collection name="batched_fractions_mzid" type="list:list">
                 <element name="pool0_batch0">
-                    <element name="inputfn0" file="empty_file1.mzid"/>
-                    <element name="inputfn1" file="empty_file2.mzid"/>
+                    <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/>
+                    <element name="inputfn1" ftype="mzid" file="empty_file2.mzid"/>
                 </element>
                 <element name="pool0_batch1">
-                    <element name="inputfn0" file="empty_file3.mzid"/>
-                    <element name="inputfn1" file="empty_file4.mzid"/>
+                    <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/>
+                    <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/>
                 </element>
             </output_collection>
         </test>
@@ -64,6 +79,7 @@
             <repeat name="poolids">
                 <param name="pool_identifier" value="set2"/>
             </repeat>
+            <param name="filetype" value="tabular" />
             <param name="listtobatch">
                 <collection type="list">
                     <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
@@ -74,16 +90,16 @@
                     <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                 </collection>
             </param>
-            <output_collection name="batched_fractions" type="list:list">
+            <output_collection name="batched_fractions_tab" type="list:list">
                 <element name="set1_batch0">
-                    <element name="inputfn0" file="empty_file1.mzid"/>
-                    <element name="inputfn1" file="empty_file2.mzid"/>
-                    <element name="inputfn2" file="empty_file3.mzid"/>
+                    <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>
                 <element name="set2_batch1">
-                    <element name="inputfn0" file="empty_file4.mzid"/>
-                    <element name="inputfn1" file="empty_file5.mzid"/>
-                    <element name="inputfn2" file="empty_file6.mzid"/>
+                    <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>
             </output_collection>
         </test>
@@ -95,6 +111,7 @@
             <repeat name="poolids">
                 <param name="pool_identifier" value="set2"/>
             </repeat>
+            <param name="filetype" value="percout" />
             <param name="listtobatch">
                 <collection type="list">
                     <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
@@ -105,20 +122,20 @@
                     <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                 </collection>
             </param>
-            <output_collection name="batched_fractions" type="list:list">
+            <output_collection name="batched_fractions_perco" type="list:list">
                 <element name="set1_batch0">
-                    <element name="inputfn0" file="empty_file1.mzid"/>
-                    <element name="inputfn1" file="empty_file2.mzid"/>
+                    <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/>
+                    <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/>
                 </element>
                 <element name="set1_batch1">
-                    <element name="inputfn0" file="empty_file3.mzid"/>
+                    <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/>
                 </element>
                 <element name="set2_batch2">
-                    <element name="inputfn0" file="empty_file4.mzid"/>
-                    <element name="inputfn1" file="empty_file5.mzid"/>
+                    <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/>
+                    <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/>
                 </element>
                 <element name="set2_batch3">
-                    <element name="inputfn0" file="empty_file6.mzid"/>
+                    <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/>
                 </element>
             </output_collection>
         </test>