--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/libshuff.xml	Fri May 19 05:22:17 2017 -0400
@@ -0,0 +1,119 @@
+<tool profile="16.07" id="mothur_libshuff" name="Libshuff" version="@WRAPPER_VERSION@.0">
+    <description>Cramer-von Mises tests communities for the same structure</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 "$dist" dist.dat &&
+        ln -s "$group" group.dat &&
+
+        echo 'libshuff(
+            phylip=dist.dat,
+            group=group.dat,
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            sim=$sim,
+            #if $form.form2 == "discrete":
+                step=$form.step,
+                #if $form.cutoff:
+                    cutoff=$form.cutoff,
+                #end if
+            #end if
+            iters=$iters
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
+        <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
+            <options>
+                <filter type="data_meta" ref="group" key="groups"/>
+            </options>
+        </param>
+        <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
+        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+        <conditional name="form">
+            <param name="form2" type="select" label="form - Select a Clustering Method" help="">
+                <option value="integral" selected="true">Integral</option>
+                <option value="discrete">Discrete</option>
+            </param>
+            <when value="integral"/>
+            <when value="discrete">
+                <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
+                <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
+        <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="forest-pasture"/>
+                    <has_text text="pasture-forest"/>
+                </assert_contents>
+            </output>
+            <output name="coverage">
+                <assert_contents>
+                    <has_text text="dist"/>
+                    <has_text text="forest-pasture"/>
+                    <has_text text="pasture-forest"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="form2" value="discrete"/>
+            <param name="step" value="0.25"/>
+            <param name="cutoff" value="0.25"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="forest-pasture"/>
+                    <has_text text="pasture-forest"/>
+                </assert_contents>
+            </output>
+            <output name="coverage">
+                <assert_contents>
+                    <has_text text="dist"/>
+                    <has_text text="forest-pasture"/>
+                    <has_text text="pasture-forest"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.
+
+.. _libshuff: https://www.mothur.org/wiki/Libshuff
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>