--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get.mimarkspackage.xml	Fri Jun 24 16:32:41 2016 -0400
@@ -0,0 +1,103 @@
+<tool profile="16.07" id="mothur_get_mimarkspackage" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
+    <description>creates a mimarks package form with your groups</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## create symlinks to input datasets
+        ln -s "$input.infile" input.infile.dat &&
+
+        echo 'get.mimarkspackage(
+            #if $input.filetype == "group":
+                group=input.infile.dat,
+            #elif $input.filetype == "oligos":
+                oligos=input.infile.dat,
+            #else:
+                file=input.infile.dat,
+            #end if
+            package=$package,
+            requiredonly=$requiredonly
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="filetype" type="select" label="input type">
+                <option value="group">group file</option>
+                <option value="oligos" selected="true">oligos file</option>
+                <option value="file">other file (e.g. output from mimarks.attributes)</option>
+            </param>
+            <when value="group">
+                <param name="infile" type="data" format="mothur.groups" label="group file"/>
+            </when>
+            <when value="oligos">
+                <param name="infile" type="data" format="mothur.oligos" label="oligos"/>
+            </when>
+            <when value="file">
+                <param name="infile" type="data" format="txt" label="file"/>
+            </when>
+        </conditional>
+        <param name="package" type="select" label="package - select the mimarks package you would like to use">
+            <option value="air">air</option>
+            <option value="host_associated">host_associated</option>
+            <option value="human_associated">human_associated</option>
+            <option value="human_gut">human_gut</option>
+            <option value="human_oral">human_oral</option>
+            <option value="human_skin">human_skin</option>
+            <option value="human_vaginal">human_vaginal</option>
+            <option value="microbial">microbial</option>
+            <option value="miscellaneous" selected="true">miscellaneous</option>
+            <option value="plant_associated">plant_associated</option>
+            <option value="sediment">sediment</option>
+            <option value="soil">soil</option>
+            <option value="wastewater">wastewater</option>
+            <option value="waterc">waterc</option>
+        </param>
+        <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/>
+    </outputs>
+    <tests>
+        <test><!-- test with group file -->
+            <param name="filetype" value="group"/>
+            <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
+            <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with oligos -->
+            <param name="filetype" value="oligos"/>
+            <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
+            <param name="package" value="human_associated"/>
+            <param name="requiredonly" value="true"/>
+            <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with other file (output from mimarks.attributes)-->
+            <param name="filetype" value="file"/>
+            <param name="infile" value="biosample.source" ftype="txt"/>
+            <output name="package_out" file="biosample.tsv" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The get.mimarkspackage_ command creates a mimarks package form with your groups.
+
+.. _get.mimarkspackage: http://www.mothur.org/wiki/Get.mimarkspackage
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>