--- a/kraken.xml	Wed Mar 23 10:55:18 2016 -0400
+++ b/kraken.xml	Mon Aug 07 17:29:06 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken" name="Kraken" version="1.2.1">
+<tool id="kraken" name="Kraken" version="@WRAPPER_VERSION@">
     <description>
         assign taxonomic labels to sequencing reads
     </description>
@@ -7,56 +7,56 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
+    <command detect_errors="exit_code">
         <![CDATA[
         @SET_DATABASE_PATH@ &&
-        kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ 
-        
-        ${only_classified_output}
+
+        kraken
+            --threads \${GALAXY_SLOTS:-1}
+            @INPUT_DATABASE@
+            ${only_classified_output}
 
-        #if str( $quick_operation.quick ) == "yes":
-            --quick
-            --min-hits ${quick_operation.min_hits}
+            #if str( $quick_operation.quick ) == "yes":
+                --quick
+                --min-hits ${quick_operation.min_hits}
 
-        #end if
+            #end if
 
-        #if $single_paired.single_paired_selector == "yes":
-            #if $forward_input.is_of_type( 'fastq' ):
-                --fastq-input
-            #else:
-                --fasta-input
-            #end if
-            "$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
+            #if $single_paired.single_paired_selector == 'yes'
+                #if $forward_input.is_of_type( 'fastq' ):
+                    --fastq-input
+                #else:
+                    --fasta-input
+                #end if
+                '${single_paired.forward_input}' '${single_paired.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}"
+                ${single_paired.check_names}
             #else:
-                --fasta-input
-            #end if
-            "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
-            ${single_paired.check_names}
-        #else:
-            #if $input_sequences.is_of_type( 'fastq' ):
-                --fastq-input
-            #else:
-                --fasta-input
+                #if $single_paired.input_sequences.is_of_type('fastq')
+                    --fastq-input
+                #else:
+                    --fasta-input
+                #end if
+                '${single_paired.input_sequences}'
             #end if
-            "$input_sequences"
-        #end if
 
-        #if $split_reads:
-            --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
-        #end if
+            #if $split_reads:
+                --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
+            #end if
 
-        ## 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
+            ## 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}" > "${translated}"
-        ]]>
-    </command>
+            > "${output}"
+            ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
+    ]]></command>
     <inputs>
         <conditional name="single_paired">
             <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
@@ -65,12 +65,12 @@
                 <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" />
-                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
+                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
+                <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
             </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"/>
+                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
+                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
                 <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="no">
@@ -78,33 +78,34 @@
             </when>
 
         </conditional>
-        <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/>
-  
+        <param name="split_reads" type="boolean" label="Output classified and unclassified reads?" help="Sets --unclassified-out and --classified-out"/>
+
         <conditional name="quick_operation">
-            <param name="quick" type="select" label="Enable quick operation?" help="--quick; Rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
+            <param argument="--quick" type="select" label="Enable quick operation"
+                   help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
                 <option value="yes">Yes</option>
                 <option selected="True" value="no">No</option>
             </param>
             <when value="yes">
-                <param name="min_hits" type="integer" value="1" label="Number of hits required for classification" help="--min-hits; min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
+                <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
+                       help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
             </when>
-            <when value="no">
-                <!-- Do absolutely nothing -->
-            </when>
+            <when value="no"/><!-- Do absolutely nothing -->
         </conditional>
 
-        <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/>
+        <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
+               label="Print no Kraken output for unclassified sequences"/>
 
         <expand macro="input_database" />
     </inputs>
     <outputs>
-        <data format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads" name="classified_out">
+        <data name="classified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
             <filter>(split_reads)</filter>
         </data>
-        <data format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">
+        <data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
             <filter>(split_reads)</filter>
         </data>
-        <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
 
@@ -116,6 +117,7 @@
             <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>
@@ -127,23 +129,6 @@
 
 -----
 
-**Kraken options**
-
-The Galaxy version of Kraken implements the following options::
-
-        
-  --fasta-input             Input is FASTA format
-  --fastq-input             Input is FASTQ format
-  --quick                   Quick operation (use first hit or hits)
-  --min-hits NUM            In quick op., number of hits req'd for classification
-                            NOTE: this is ignored if --quick is not specified
-  --unclassified-out        Print unclassified sequences to filename
-  --classified-out          Print classified sequences to filename
-
-  --only-classified-output  Print no Kraken output for unclassified sequences
-                          
-------
-
 **Output Format**
 
 Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are::