--- a/mimarks.attributes.xml	Tue Sep 05 16:50:06 2017 -0400
+++ b/mimarks.attributes.xml	Tue Mar 20 21:57:39 2018 -0400
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
+<tool profile="16.07" id="mothur_mimarks_attributes" name="Mimarks.attributes" version="@WRAPPER_VERSION@.0">
     <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description>
     <macros>
         <import>macros.xml</import>
@@ -7,17 +7,17 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$biosample_in" biosample_in.dat &&
+## create symlinks to input datasets
+ln -s '$biosample_in' biosample_in.dat &&
 
-        echo 'mimarks.attributes(
-            xml=biosample_in.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'mimarks.attributes(
+    xml=biosample_in.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
@@ -25,6 +25,7 @@
         <param name="package" type="select" label="package - select the mimarks package you would like to use">
             <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
         </param>-->
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -34,20 +35,23 @@
         <test>
             <param name="biosample_in" value="biosample.xml" ftype="xml"/>
             <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command.
+The mimarks.attributes_ command reads `BioSample Attributes`_ xml and generates source for get.mimarkspackage_ command.
 
-]]>
-    </help>
+.. _mimarks.attributes: https://www.mothur.org/w/index.php?search=mimarks.attributes
+.. _BioSample Attributes: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
+.. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
+
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>