--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify.rf.xml	Fri May 19 05:14:41 2017 -0400
@@ -0,0 +1,100 @@
+<tool profile="16.07" id="mothur_classify_rf" name="Classify.rf" 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 '$otu' shared.dat &&
+        ln -s '$design' design.dat &&
+
+        echo 'classify.rf(
+            shared=shared.dat,
+            design=design.dat
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+            #if $otupersplit:
+                ,otupersplit=$otupersplit
+            #end if
+            #if $seed:
+                ,seed=$seed
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+        <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
+        <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" multiple="true" optional="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="otupersplit" type="select" optional="true" label="otupersplit">
+            <option value="log2">log2</option>
+            <option value="squareroot">square root</option>
+        </param>
+        <param name="seed" type="integer" value="" min="0" optional="true" label="seed" help="Will be randomly chosen if left blank"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="summary" format="tabular" from_work_dir="shared.RF*summary" label="${tool.name} on ${on_string}: summary"/>
+        <data name="misclass-summary" format="tabular" from_work_dir="shared.misclassifications*.summary" label="${tool.name} on ${on_string}: misclassifications summary"/>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
+            <param name="design" value="mouse.design"/>
+            <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
+            <output name="misclass-summary" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="Sample\tRF classification\tActual classification"/>
+                    <has_text text="F003D000"/>
+                    <has_text text="F003D150"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with custom settings -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
+            <param name="design" value="mouse.design"/>
+            <param name="label" value="1"/>
+            <param name="otupersplit" value="log2"/>
+            <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142,F003D144,F003D146,F003D148"/>
+            <param name="seed" value="42"/> <!-- tool will unpredictable segfault without this -->
+            <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
+            <output name="misclass-summary" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="Sample\tRF classification\tActual classification"/>
+                    <has_text text="F003D000"/>
+                    <not_has_text text="F003D150"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+
+.. _classify.rf: https://www.mothur.org/wiki/Classify.rf
+    ]]></help>
+    <expand macro="citations"/>
+</tool>