--- a/kraken.xml	Tue May 19 16:41:06 2015 -0400
+++ b/kraken.xml	Wed Jul 15 14:59:31 2015 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="kraken" name="Kraken" version="1.0.0">
+<tool id="kraken" name="Kraken" version="1.1.0">
     <description>
-        assign taxonomic labels to short DNA reads
+        assign taxonomic labels to sequencing reads
     </description>
     <macros>
         <import>macros.xml</import>
@@ -10,17 +10,49 @@
         <![CDATA[
         @SET_DATABASE_PATH@ &&
         kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ 
+        
+        #if $input_sequences.is_of_type( 'fastq' ):
+            --fastq-input
+        #else:
+            --fasta-input
+        #end if
+
+        ${only_classified_output}
+
+        #if str( $quick_operation.quick ) == "yes":
+            --quick
+            --min-hits ${quick_operation.min_hits}
+
+        #end if
+
         "$input_sequences"
+
         #if $split_reads:
             --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
         #end if
-        --output "${output}" &&
-        kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
+        --output "${output}"
+        ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
         ]]>
     </command>
     <inputs>
-        <param format="fasta,fastq,fastqsanger" label="Input sequences" name="input_sequences" type="data" />
-        <param label="Output classified and unclassified reads" name="split_reads" type="boolean" />
+        <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
+        <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/>
+  
+        <conditional name="quick_operation">
+            <param name="quick" type="select" label="Enable quick operation?" help="--quick; Rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
+                <option value="yes">Yes</option>
+                <option selected="True" value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="min_hits" type="integer" value="1" label="Number of hits required for classification" help="--min-hits; min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
+            </when>
+            <when value="no">
+                <!-- Do absolutely nothing -->
+            </when>
+        </conditional>
+
+        <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/>
+
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -30,57 +62,43 @@
         <data format="tabular" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">
             <filter>(split_reads)</filter>
         </data>
-        <data format="tabular" label="${tool.name} on ${on_string}: Histogram" name="histogram">
-            <filter>(draw_histogram)</filter>
-        </data>
         <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
-        <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
+        <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
     <help>
         <![CDATA[
-        **What it does**
-
-        Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise. Our tests on various real and simulated data have shown Kraken to have sensitivity slightly lower than Megablast with precision being slightly higher. On a set of simulated 100 bp reads, Kraken processed over 1.3 million reads per minute on a single core in normal operation, and over 4.1 million reads per minute in quick operation.
+**What it does**
 
-        **Usage**
-
-        Kraken classifies a set of sequences (reads) with the commands below:
-
-        kraken --db $DBNAME sequences.fa > sequences.kraken
+Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.
 
-        or
-
-        kraken --db $DBNAME sequences.fq > sequences.kraken
-
+-----
 
-        -DBNAME is the name of the Kraken Database to be used.
+**Kraken options**
 
-        -sequences.fa or sequences.fq is the FASTA or FASTQ input file containing the desired sequences for classification.
-
-        -sequences.kraken is the generated output.
-
+The Galaxy version of Kraken implements the following options::
 
-
-        **Options**
-
-        The kraken program allows several different sequencing modifiers (parameters):
-
-        **Multithreading:** Use the --threads NUM switch to use multiple threads.
-
-        **Sequence filtering:** Classified or unclassified sequences can be sent to a file for later processing, using the --classified-out and --unclassified-out switches, respectively.
-
-
+        
+  --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
 
-        **Output Format**
+  --only-classified-output  Print no Kraken output for unclassified sequences
+                          
+------
 
-        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:
+**Output Format**
 
-        1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
-        2. The sequence ID, obtained from the FASTA/FASTQ header.
-        3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
-        4. The length of the sequence in bp.
+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::
 
-        5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
+    1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
+    2. The sequence ID, obtained from the FASTA/FASTQ header.
+    3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
+    4. The length of the sequence in bp.
+    5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
             a) the first 13 k-mers mapped to taxonomy ID #562
             b) the next 4 k-mers mapped to taxonomy ID #561
             c) the next 31 k-mers contained an ambiguous nucleotide
@@ -92,4 +110,4 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <expand macro="citations" />
-</tool>
\ No newline at end of file
+</tool>