--- a/kraken.xml	Thu Nov 05 10:10:05 2015 -0500
+++ b/kraken.xml	Fri Dec 18 19:41:02 2015 -0500
@@ -1,11 +1,14 @@
 <?xml version="1.0"?>
-<tool id="kraken" name="Kraken" version="1.1.2">
+<tool id="kraken" name="Kraken" version="1.1.3">
     <description>
         assign taxonomic labels to sequencing reads
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
         <![CDATA[
         @SET_DATABASE_PATH@ &&
@@ -47,7 +50,10 @@
         #if $split_reads:
             --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
         #end if
-        --output "${output}"
+
+        ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
+
+        > "${output}"
         ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
         ]]>
     </command>
@@ -55,8 +61,8 @@
         <conditional name="single_paired">
             <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
                 <option value="collection">Collection</option>
-                <option value="yes">Yes</option>
-                <option selected="True" value="no">No</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
             </param>
             <when value="collection">
                 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" />
@@ -101,6 +107,18 @@
         <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
+
+    <tests>
+        <test>
+            <param name="single_paired_selector" value="no"/>
+            <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
+            <param name="split_reads" value="false"/>
+            <param name="quick" value="no"/>
+            <param name="only-classified-output" value="false"/>
+            <param name="kraken_database" value="test_db"/>
+            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
+        </test>
+    </tests>
     <help>
         <![CDATA[
 **What it does**
@@ -142,8 +160,5 @@
             e) the last 3 k-mers mapped to taxonomy ID #562
         ]]>
     </help>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
     <expand macro="citations" />
 </tool>