--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmds.xml	Fri May 19 05:33:06 2017 -0400
@@ -0,0 +1,84 @@
+<tool profile="16.07" id="mothur_nmds" name="Nmds" version="@WRAPPER_VERSION@.0">
+    <description>generate non-metric multidimensional scaling data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$dist" dist.dat &&
+        ln -s "$axes" axes.dat &&
+
+        echo 'nmds(
+            phylip=dist.dat
+            #if $axes:
+                ,axes=axes.dat
+            #end if
+            ,mindim=$mindim
+            #if $maxdim >= $mindim:
+                ,maxdim=$maxdim
+            #end if
+            ,iters=$iters
+            ,maxiters=$maxiters
+
+            ## Mothur can't cope with scientific notation
+            #set epsilon_decimal = "{:.12f}".format(float($epsilon))
+            ,epsilon=$epsilon_decimal
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param name="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
+        <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
+        <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
+        <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
+        <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
+        <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="nmds_axes" format="mothur.axes" from_work_dir="dist*.axes" label="${tool.name} on ${on_string}: nmds.axes"/>
+        <data name="nmds_iters" format="tabular" from_work_dir="dist*.iters" label="${tool.name} on ${on_string}: nmds.iters"/>
+        <data name="nmds_stress" format="tabular" from_work_dir="dist*.stress" label="${tool.name} on ${on_string}: nmds.stress"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dist" value="amazon.dist"/>
+            <param name="axes" value="amazon.pcoa.axes"/>
+            <param name="mindim" value="1"/>
+            <param name="maxdim" value="2"/>
+            <param name="iters" value="10"/>
+            <param name="maxiters" value="500"/>
+            <param name="epsilon" value="1e-12"/>
+            <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
+            <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
+            <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+.. _Mothur: https://www.mothur.org/wiki/Main_Page
+
+**Command Documentation**
+
+The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.
+
+.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _nmds: https://www.mothur.org/wiki/Nmds
+
+v1.20.0: Updated to mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>