--- a/cluster.fragments.xml	Tue Sep 05 17:03:19 2017 -0400
+++ b/cluster.fragments.xml	Tue Mar 20 22:22:06 2018 -0400
@@ -7,33 +7,36 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$names" names.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$names' names.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'cluster.fragments(
-            fasta=fasta.dat,
-            diffs=$diffs,
-            percent=$percent,
-            #if $count:
-                count=count.dat,
-            #end if
-            name=names.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'cluster.fragments(
+    fasta=fasta.dat,
+    diffs=$diffs,
+    percent=$percent,
+    #if $count:
+        count=count.dat,
+    #end if
+    name=names.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
-        <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
-        <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
-        <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
-               help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
+        <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param argument="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
+        <param argument="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
+               help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less
+               than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like:
+               If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -46,11 +49,11 @@
             <param name="names" value="amazon1.names" ftype="mothur.names"/>
             <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
             <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -62,7 +65,6 @@
 
 v1.21: Updated to Mothur 1.33. Added count parameter.
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>