--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.shared.xml	Fri May 19 05:08:32 2017 -0400
@@ -0,0 +1,127 @@
+<tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0">
+    <description>Make a shared file from a list and a group</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 "$intype.otu" intype_otu.dat &&
+        #if $intype.infile == "otulist":
+            ln -s "$intype.group" intype_group.dat &&
+        #end if
+
+        echo 'make.shared(
+            #if $intype.infile == "biom":
+                biom=intype_otu.dat
+            #else
+                #if $intype.group.is_of_type("mothur.groups"):
+                    group=intype_group.dat,
+                #elif $intype.group.is_of_type("mothur.count_table"):
+                    count=intype_group.dat,
+                #end if
+                #if $intype.label:
+                    label=${ str($intype.label).replace(",","-") },
+                #end if
+                #if $intype.groups:
+                    groups=${ str($intype.groups).replace(",","-") },
+                #end if
+                list=intype_otu.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log &&
+
+        ## move output files to correct destination
+        mv mothur.*.logfile "$logfile" &&
+        #if $intype.infile == 'otulist' and $intype.groups:
+            mv intype_otu*.groups "$groupout"
+        #else
+            mv intype_otu*.shared "$shared"
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="intype">
+            <param name="infile" type="select" label="Select input type" help="">
+                <option value="otulist">OTU list</option>
+                <option value="biom">Biom 1.0 file</option>
+            </param>
+            <when value="otulist">
+                <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+                <param name="group" type="data" format="mothur.groups, mothur.count_table" label="supply group or count table if you supplied OTU list"/>
+                <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
+                    <expand macro="labeloptions"/>
+                </param>
+                <param name="groups" type="select" multiple="true" label="groups - Groups to include">
+                    <options>
+                        <filter type="data_meta" ref="group" key="groups"/>
+                    </options>
+                </param>
+            </when>
+            <when value="biom">
+                <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
+        <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
+            <filter>intype['group'].ext == "mothur.groups"</filter>
+        </data>
+        <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
+            <filter>intype['groups']</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with biom file -->
+            <param name="infile" value="biom"/>
+            <param name="otu" value="example.biom"/>
+            <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with otu and group file-->
+            <param name="infile" value="otulist"/>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with label and group select-->
+            <param name="infile" value="otulist"/>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="label" value="0.03,0.05,0.22"/>
+            <param name="groups" value="forest,pasture"/>
+            <output name="groupout" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <output_collection name="labelshares" count="3">
+                <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.
+
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _make.shared: https://www.mothur.org/wiki/Make.shared
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>