--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get.communitytype.xml	Fri May 19 05:34:30 2017 -0400
@@ -0,0 +1,157 @@
+<tool profile="16.07" id="mothur_get_communitytype" name="Get.communitytype" version="@WRAPPER_VERSION@.0">
+    <description>description</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 '$otu' shared.dat &&
+
+        echo 'get.communitytype(
+            shared=shared.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            method=$m.method,
+            #if $m.method == 'kmeans' or $m.method == 'pams':
+                calc=$m.calc,
+                iters=$m.iters,
+            #end if
+            #if int($subsample) == 0:
+                subsample=T,
+            #elif int($subsample) > 0:
+                subsample=$subsample,
+            #end if
+            minpartitions=$minpartitions,
+            maxpartitions=$maxpartitions,
+            optimizegap=$optimizegap,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" label="groups - Groups to consider" multiple="true" optional="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <conditional name="m">
+            <param name="method" type="select" label="method">
+                <option value="dmm" selected="true">dmm</option>
+                <option value="kmeans">k means</option>
+                <option value="pam">pam</option>
+            </param>
+            <when value="dmm"/>
+            <when value="kmeans">
+                <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
+                    <expand macro="calc-common"/>
+                    <!-- set default option(s) -->
+                    <option value="rjsd" selected="true">rjsd</option>
+                </param>
+                <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
+            </when>
+            <when value="pam">
+                <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
+                    <expand macro="calc-common"/>
+                    <!-- set default option -->
+                    <option value="rjsd" selected="true">rjsd</option>
+                </param>
+                <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
+            </when>
+        </conditional>
+        <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/>
+        <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/>
+        <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/>
+        <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary">
+            <filter> m['method'] == 'dmm' </filter>
+        </data>
+        <data name="design" format="tabular" from_work_dir="shared*.design" label="${tool.name} on ${on_string}: design"/>
+        <data name="parameters" format="tabular" from_work_dir="shared*.parameters" label="${tool.name} on ${on_string}: parameters">
+            <filter> m['method'] == 'dmm' </filter>
+        </data>
+        <data name="fit" format="tabular" from_work_dir="shared*.fit" label="${tool.name} on ${on_string}: fit"/>
+        <collection name="relabund" type="list" label="${tool.name} on ${on_string}: relabund">
+            <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.relabund" format="mothur.relabund"/>
+        </collection>
+        <collection name="posterior" type="list" label="${tool.name} on ${on_string}: posterior">
+            <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.posterior" format="tabular"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared"/>
+            <output name="summary" md5="3e81c01da5f6c86b69516e204ad51610" ftype="tabular"/>
+            <output name="design" md5="df00e5ea21154669bbb85efa20a9661d" ftype="tabular"/>
+            <output name="parameters" md5="ef972523811b80b12d4343f0df472214" ftype="tabular"/>
+            <output name="fit" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="K\tNLE\tlogDet\tBIC\tAIC\tLaplace"/>
+                </assert_contents>
+            </output>
+            <output_collection name="relabund" count="5">
+                <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/>
+            </output_collection>
+            <output_collection name="posterior" count="5">
+                <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with all settings -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
+            <param name="label" value="1"/>
+            <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142"/>
+            <param name="method" value="kmeans"/>
+            <param name="iters" value="100"/>
+            <param name="calc" value="manhattan"/>
+            <param name="maxpartitions" value="4"/>
+            <param name="subsample" value="0"/>
+            <output name="design" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Partition_"/>
+                    <has_text text="F003D000"/>
+                    <has_text text="F003D142"/>
+                </assert_contents>
+            </output>
+            <output name="fit" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="K\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142"/>
+                </assert_contents>
+            </output>
+            <output_collection name="relabund" count="4">
+                <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/>
+            </output_collection>
+            <output_collection name="posterior" count="4">
+                <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+
+.. _get.communitytype: https://www.mothur.org/wiki/Get.communitytype
+    ]]></help>
+    <expand macro="citations"/>
+</tool>