# HG changeset patch
# User devteam
# Date 1446736180 18000
# Node ID bc918f32d4be18ecc1b0bb7fe32a8ac8e5d8f215
# Parent  55d42997c0b5abb16176f0c81a6326dca323e307
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 4782f9ad9bfe2479685ccaf51b66b0d32f83f193

diff -r 55d42997c0b5 -r bc918f32d4be kraken.xml
--- a/kraken.xml	Wed Nov 04 10:09:27 2015 -0500
+++ b/kraken.xml	Thu Nov 05 10:09:40 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_collection1" 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"/>