--- a/chop.seqs.xml	Fri Sep 08 14:54:33 2017 -0400
+++ b/chop.seqs.xml	Tue Mar 20 22:22:50 2018 -0400
@@ -7,47 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$name' name.dat &&
+ln -s '$group' group.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'chop.seqs(
-            fasta=fasta.dat,
-            numbases=$numbases,
-            keep=$keep,
-            countgaps=$countgaps,
-            short=$short,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $group:
-                group=group.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chop.seqs(
+    fasta=fasta.dat,
+    numbases=$numbases,
+    keep=$keep,
+    countgaps=$countgaps,
+    short=$short,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $group:
+        group=group.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
-        <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
-        <param name="keep" type="select" label="keep - Part of the sequence to keep">
+        <param argument="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
+        <param argument="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
+        <param argument="keep" type="select" label="keep - Part of the sequence to keep">
             <option value="front">front</option>
             <option value="back">back</option>
         </param>
-        <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
-        <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
-        <param name="name" type="data" format="mothur.names" optional="true"  label="name file"/>
-        <param name="group" type="data" format="mothur.groups" optional="true" label="group file"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
+        <param argument="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
+        <param argument="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
+        <param argument="name" type="data" format="mothur.names" optional="true"  label="name file"/>
+        <param argument="group" type="data" format="mothur.groups" optional="true" label="group file"/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -58,11 +59,11 @@
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
             <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -73,7 +74,7 @@
 .. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs
 
 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>