--- a/get.mimarkspackage.xml	Tue Sep 05 16:56:28 2017 -0400
+++ b/get.mimarkspackage.xml	Tue Mar 20 22:25:46 2018 -0400
@@ -7,23 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.infile" input.infile.dat &&
+## create symlinks to input datasets
+ln -s '$input.infile' input.infile.dat &&
 
-        echo 'get.mimarkspackage(
-            #if $input.filetype == "group":
-                group=input.infile.dat,
-            #elif $input.filetype == "oligos":
-                oligos=input.infile.dat,
-            #end if
-            package=$package,
-            requiredonly=$requiredonly
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.mimarkspackage(
+    #if $input.filetype == "group":
+        group=input.infile.dat,
+    #elif $input.filetype == "oligos":
+        oligos=input.infile.dat,
+    #end if
+    package=$package,
+    requiredonly=$requiredonly
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -55,6 +55,7 @@
             <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"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -65,6 +66,7 @@
             <param name="filetype" value="group"/>
             <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
             <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with oligos -->
@@ -73,11 +75,11 @@
             <param name="package" value="human_associated"/>
             <param name="requiredonly" value="true"/>
             <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -87,8 +89,7 @@
 
 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>