--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.lefse.xml	Fri May 19 05:38:38 2017 -0400
@@ -0,0 +1,86 @@
+<tool profile="16.07" id="mothur_make_lefse" name="Make.lefse" version="@WRAPPER_VERSION@.0">
+    <description>create a lefse formatted input file from mothur's output files</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 "$otu" otu.dat &&
+        ln -s "$design" design.dat &&
+        ln -s "$constaxonomy" constaxonomy.dat &&
+
+        echo 'make.lefse(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=otu.dat,
+            #else
+                shared=otu.dat,
+            #end if
+            #if $design:
+                design=design.dat,
+            #end if
+            #if $constaxonomy:
+                constaxonomy=constaxonomy.dat,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            scale=$scale
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
+        <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="constaxonomy - provide a constaxonomy file"/>
+        <param name="design" type="data" format="tabular" optional="true" label="design - provide your design file"/>
+        <param name="scale" type="select" multiple="false" label="scale - select what scale you would like to use to convert your shared file abundances to relative abundances" help="">
+            <option value="totalgroup" selected="true">totalgroup</option>
+            <option value="totalotu">totalotu</option>
+            <option value="averagegroup">averagegroup</option>
+            <option value="averageotu">averageotu</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/>
+    </outputs>
+    <tests>
+        <test><!-- test with shared file and defaults -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with relabund file -->
+            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
+            <param name="design" value="toymothur.design2" ftype="tabular"/>
+            <param name="label" value="0.18"/>
+            <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
+
+.. _make.lefse: https://www.mothur.org/wiki/Make.lefse
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>