--- a/sens.spec.xml	Tue Sep 05 16:57:47 2017 -0400
+++ b/sens.spec.xml	Tue Mar 20 21:54:54 2018 -0400
@@ -7,31 +7,69 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$dist" dist.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$matrix.dist' matrix.dist.dat &&
+#if str($matrix.method_name.method) == "count" :
+        ln -s '$matrix.method_name.count' matrix.method_name.count.dat &&
+#else
+       ln -s '$matrix.method_name.names' matrix.method_name.names.dat &&
+#end if
+
 
-        echo 'sens.spec(
-            list=otu.dat,
-            #if $dist.is_of_type("mothur.dist"):
-                column=dist.dat,
-            #else
-                phylip=dist.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            precision=$precision,
-            cutoff=$cutoff,
-            hard=$hard
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'sens.spec(
+    list=otu.dat,
+    #if str($matrix.format) == "phylip":
+        phylip=matrix.dist.dat,
+    #else
+        column=matrix.dist.dat,
+    #end if
+    #if str($matrix.method_name.method) == "count" :
+       count=matrix.method_name.count.dat,
+    #else
+       names=matrix.method_name.names.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    precision=$precision,
+    cutoff=$cutoff
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
+	<conditional name="matrix">
+                <param name="format" type="select" label="Select a Distance Matrix Format" help="">
+                        <option value="column">Pairwise Column Matrix </option>
+                        <option value="phylip">Phylip Distance Matrix</option>
+                </param>
+                <when value="column">
+                        <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
+                        <conditional name="method_name">
+                                <param name="method" type="select" label="Select a Method" help="">
+                                        <option value="count">count file associated with your distance matrix.</option>
+                                        <option value="name">name file associated with your distance matrix. </option>
+                                </param>
+                                <when value="count">
+                                        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+                                </when>
+                                <when value="name">
+                                        <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+                                </when>
+
+                        </conditional>
+                </when>
+                <when value="phylip">
+                        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                </when>
+         </conditional>
         <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
         <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
         <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
@@ -41,7 +79,7 @@
         </param>
         <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
         <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
-        <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -49,22 +87,26 @@
     </outputs>
     <tests>
         <test>
-            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+	<param name="count" value="amazon.count_table"/>
+	<param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
-            <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/>
+            <output name="sensspec" md5="720789a7ef4da26928a61161279d7344" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
+	    <param name="count" value="amazon.count_table"/>
+	    <param name="names" value="amazon.names"/>
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
             <param name="cutoff" value="0.10"/>
             <param name="label" value="0.03,0.05,0.22"/>
-            <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/>
+            <output name="sensspec" md5="3992dec1d799ec3a061b3ef713a58382" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -77,7 +119,7 @@
 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>