--- a/sort.seqs.xml	Tue Sep 05 17:05:44 2017 -0400
+++ b/sort.seqs.xml	Tue Mar 20 22:04:32 2018 -0400
@@ -7,48 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta_in" fasta_in.dat &&
-        ln -s "$qfile_in" qfile_in.dat &&
-        ln -s "$flow_in" flow_in.dat &&
-        ln -s "$name_in" name_in.dat &&
-        ln -s "$group_in" group_in.dat &&
-        ln -s "$tax_in" tax_in.dat &&
-        ln -s "$accnos" accnos.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$qfile_in' qfile_in.dat &&
+ln -s '$flow_in' flow_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$group_in' group_in.dat &&
+ln -s '$tax_in' tax_in.dat &&
+ln -s '$accnos' accnos.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'sort.seqs(
-            #if $fasta_in:
-                fasta=fasta_in.dat,
-            #end if
-            #if $qfile_in:
-                qfile=qfile_in.dat,
-            #end if
-            #if $flow_in:
-                flow=flow_in.dat,
-            #end if
-            #if $name_in:
-                name=name_in.dat,
-            #end if
-            #if $group_in:
-                group=group_in.dat,
-            #end if
-            #if $tax_in:
-                taxonomy=tax_in.dat,
-            #end if
-            #if $accnos:
-                accnos=accnos.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            large=$large
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'sort.seqs(
+    #if $fasta_in:
+        fasta=fasta_in.dat,
+    #end if
+    #if $qfile_in:
+        qfile=qfile_in.dat,
+    #end if
+    #if $flow_in:
+        flow=flow_in.dat,
+    #end if
+    #if $name_in:
+        name=name_in.dat,
+    #end if
+    #if $group_in:
+        group=group_in.dat,
+    #end if
+    #if $tax_in:
+        taxonomy=tax_in.dat,
+    #end if
+    #if $accnos:
+        accnos=accnos.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    large=$large
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
@@ -60,6 +60,7 @@
         <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/>
         <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -86,22 +87,26 @@
         <test>
             <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
             <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
             <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
             <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
             <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
             <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with multiple file types input -->
@@ -111,11 +116,11 @@
             <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
             <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
             <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -126,7 +131,6 @@
 
 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>