# HG changeset patch
# User devteam
# Date 1447264249 18000
# Node ID 642f30185af2331cca4bd6b000393bc51ededb15
# Parent  7b3ef9b4af806a9441c81bea575a3215c26918ba
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7

diff -r 7b3ef9b4af80 -r 642f30185af2 kraken.xml
--- a/kraken.xml	Wed Nov 04 09:47:00 2015 -0500
+++ b/kraken.xml	Wed Nov 11 12:50:49 2015 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken" name="Kraken" version="1.1.1">
+<tool id="kraken" name="Kraken" version="1.1.2">
     <description>
         assign taxonomic labels to sequencing reads
     </description>
@@ -27,6 +27,14 @@
             #end if
             "$forward_input" "$reverse_input"
             ${single_paired.check_names}
+        #elif $single_paired.single_paired_selector == "collection":
+            #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
+                --fastq-input
+            #else:
+                --fasta-input
+            #end if
+            "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
+            ${single_paired.check_names}
         #else:
             #if $input_sequences.is_of_type( 'fastq' ):
                 --fastq-input
@@ -45,10 +53,15 @@
     </command>
     <inputs>
         <conditional name="single_paired">
-            <param name="single_paired_selector" type="select" label="Reads are paired-end" help="--paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+                <option value="collection">Collection</option>
                 <option value="yes">Yes</option>
                 <option selected="True" value="no">No</option>
             </param>
+            <when value="collection">
+                <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" />
+                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
+            </when>
             <when value="yes">
                 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/>
                 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/>