--- a/remove.otulabels.xml	Tue Sep 05 17:04:10 2017 -0400
+++ b/remove.otulabels.xml	Tue Mar 20 22:22:34 2018 -0400
@@ -7,36 +7,36 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$infile.otu" infile.otu.dat &&
-        ln -s "$accnos" accnos.dat &&
+## create symlinks to input datasets
+ln -s '$infile.otu' infile.otu.dat &&
+ln -s '$accnos' accnos.dat &&
 
-        echo 'remove.otulabels(
-            #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
-                constaxonomy=infile.otu.data,
-            #end if
-            #if $infile.otu.is_of_type("mothur.otu.corr"):
-                otucorr=infile.otu.dat,
-            #end if
-            #if $infile.otu.is_of_type("mothur.axes"):
-                corraxes=infile.otu.dat,
-            #end if
-            #if $infile.otu.is_of_type("mothur.list"):
-                list=infile.otu.dat,
-            #end if
-            #if $infile.otu.is_of_type("mothur.shared"):
-                shared=infile.otu.dat,
-            #end if
-            #if $infile.intype == "in_shared" and $infile.label:
-                label=${ str($infile.label).replace(",","-") },
-            #end if
-            accnos=accnos.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'remove.otulabels(
+    #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
+        constaxonomy=infile.otu.data,
+    #end if
+    #if $infile.otu.is_of_type("mothur.otu.corr"):
+        otucorr=infile.otu.dat,
+    #end if
+    #if $infile.otu.is_of_type("mothur.axes"):
+        corraxes=infile.otu.dat,
+    #end if
+    #if $infile.otu.is_of_type("mothur.list"):
+        list=infile.otu.dat,
+    #end if
+    #if $infile.otu.is_of_type("mothur.shared"):
+        shared=infile.otu.dat,
+    #end if
+    #if $infile.intype == "in_shared" and $infile.label:
+        label=${ str($infile.label).replace(",","-") },
+    #end if
+    accnos=accnos.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
@@ -55,6 +55,7 @@
                 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -66,19 +67,32 @@
             <param name="intype" value="in_shared"/>
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="label" value="0.22"/>
-            <output name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/>
+            <output name="pick_out" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="U68686"/>
+                    <has_text text="0.22"/>
+                    <not_has_text text="0.03"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with constaxonomy/otucorr/corraxes file -->
             <param name="accnos" value="amazon.accnos.otulabels"/>
             <param name="intype" value="in_other"/>
             <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
-            <output name="pick_out" md5="9bffef40bf6e879737835cf7323c5ce4" ftype="mothur.axes"/>
+            <output name="pick_out" ftype="mothur.axes">
+                <assert_contents>
+                    <expand macro="test-axes-format"/>
+                    <has_text text="U68686"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -90,7 +104,7 @@
 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
 .. _otu.association: https://www.mothur.org/wiki/Otu.association
 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>