--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.files.xml	Fri May 19 05:10:40 2017 -0400
@@ -0,0 +1,76 @@
+<tool profile="16.07" id="mothur_merge_files" name="Merge.files" version="@WRAPPER_VERSION@.0">
+    <description>Merge 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
+        #for $i in $merge.inputs:
+            ln -s "$i" input${merge.inputs.index($i)}.dat &&
+        #end for
+
+        echo 'merge.files(
+            input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
+            output=$output
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | sed 's/-,/,/g'
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+    <conditional name="merge">
+        <param name="type" type="select" format="fasta,qual,mothur.groups,mothur.names,mothur.accnos" label="Merge">
+            <option value="fasta">fasta files</option>
+            <option value="qual">qual files</option>
+            <option value="groups">group files</option>
+            <option value="names">name files</option>
+            <option value="accnos">accnos files</option>
+        </param>
+        <when value="fasta">
+            <param name="inputs" type="data" format="fasta" multiple="true" label="inputs - fasta"/>
+        </when> <!-- fasta -->
+        <when value="qual">
+            <param name="inputs" type="data" format="qual" multiple="true" label="inputs - qual"/>
+        </when> <!-- qual -->
+        <when value="groups">
+            <param name="inputs" type="data" format="mothur.groups" multiple="true" label="inputs - groups"/>
+        </when> <!-- groups -->
+        <when value="names">
+            <param name="inputs" type="data" format="mothur.names" multiple="true" label="inputs - names"/>
+        </when> <!-- names -->
+        <when value="accnos">
+            <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
+        </when> <!-- fasta -->
+    </conditional> <!-- merge -->
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="type" value="fasta"/>
+            <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
+            <output name="output" file="output.fa" ftype="fasta"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The merge.files_ command merge inputs into a single output.
+
+.. _merge.files: https://www.mothur.org/wiki/Merge.files
+
+
+    </help>
+     <expand macro="citations"/>
+</tool>