--- a/get.mimarkspackage.xml	Fri Jun 24 16:32:41 2016 -0400
+++ b/get.mimarkspackage.xml	Fri May 19 05:27:47 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$input.infile" input.infile.dat &&
 
@@ -14,21 +17,19 @@
                 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
+        | tee mothur.out.log
     ]]></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"/>
@@ -36,9 +37,6 @@
             <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>
@@ -77,23 +75,17 @@
             <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**
+**Command Documentation**
 
 The get.mimarkspackage_ command creates a mimarks package form with your groups.
 
-.. _get.mimarkspackage: http://www.mothur.org/wiki/Get.mimarkspackage
+.. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
 
 ]]>
     </help>