--- a/kma_map.xml	Fri Oct 04 15:46:45 2019 -0400
+++ b/kma_map.xml	Wed Feb 05 00:58:24 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">
+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@_galaxy0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -19,8 +19,36 @@
             #else:
                 -i '${single_paired.input_sequences}'
             #end if
-            -o output &&
-	 gunzip output.frag.gz
+            #if str($settings.advanced) == "advanced"
+              #if str($settings.kmer_size)
+                -k '${settings.kmer_size}'
+              #end if
+              #if str($settings.p_value)
+                -p '${settings.p_value}'
+              #end if
+              ${settings.decontaminate}
+              ${settings.dense}
+              ${settings.ref_fsa}
+              ${settings.matrix}
+              ${settings.all_best_mappings}
+              #if str($settings.minimum_phred_score)
+                -mp '${settings.minimum_phred_score}'
+              #end if
+              #if str($settings.cut_5_prime)
+                -5p '${settings.cut_5_prime}'
+              #end if
+              ${settings.only_count_kmers}
+              #if str($settings.min_id)
+                -ID '${settings.min_id}'
+              #end if
+              ${settings.force_end_to_end}
+            #end if
+            -o output
+	 
+        #if str($settings.advanced) == "advanced" and $settings.matrix
+            && gunzip output.mat.gz
+        #end if
+        && gunzip output.frag.gz
 	]]>
     </command>
     <inputs>
@@ -41,19 +69,67 @@
                 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
             </when>
         </conditional>
+
 	<param name="kma_index" type="select">
 	    <options from_data_table="kma_index">
 	        <validator type="no_options" message="No KMA index available" />
             </options>
         </param>
+        
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Specify advanced parameters">
+                <option value="simple" selected="true">No, use program defaults.</option>
+                <option value="advanced">Yes, see full parameter list.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+                <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
+                <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
+                <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
+                <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
+                <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
+                <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
+                <param name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Print assembly matrix" />
+                <param name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
+                <param name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
+                <param name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
+                <param name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
+                <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
+                <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
       <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />
-      <data name="consensus_alignment" label="Consensus alignment" format="text" from_work_dir="output.aln" />
+      <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" />
       <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" />
       <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" />
+      <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat">
+          <filter>settings['matrix']</filter>
+      </data>
     </outputs>
     <tests>
+        <test>
+            <param name="single_paired_selector" value="no"/>
+            <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
+            <param name="advanced" value="advanced"/>
+            <param name="kmer_size" value="8"/>
+            <param name="kma_index" value="test_index"/>
+            <output name="result_overview" file="ERR884056.res" ftype="tabular"/>
+            <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/>
+            <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/>
+            <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="single_paired_selector" value="no"/>
+            <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
+            <param name="advanced" value="advanced"/>
+            <param name="kmer_size" value="8"/>
+            <param name="matrix" value="true"/>
+            <param name="kma_index" value="test_index"/>
+            <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/>
+        </test>
     </tests>
     <help>
       <![CDATA[