--- a/pcr.seqs.xml	Tue Sep 05 16:27:35 2017 -0400
+++ b/pcr.seqs.xml	Wed Feb 14 09:38:08 2018 -0500
@@ -7,54 +7,53 @@
     <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_in" name_in.dat &&
-        ln -s "$group_in" group_in.dat &&
-        ln -s "$taxonomy_in" taxonomy_in.dat &&
-        #if $trim.method == "oligos":
-            ln -s "$trim.oligos" trim.oligos.dat &&
-        #elif $trim.method == "reference":
-            ln -s "$trim.ecoli" trim.ecoli.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$group_in' group_in.dat &&
+ln -s '$taxonomy_in' taxonomy_in.dat &&
+#if $trim.method == "oligos":
+    ln -s '$trim.oligos' trim.oligos.dat &&
+#elif $trim.method == "reference":
+    ln -s '$trim.ecoli' trim.ecoli.dat &&
+#end if
 
-        echo 'pcr.seqs(
-            fasta=fasta.dat,
-            #if $name_in
-                name=name_in.dat,
-            #end if
-            #if $group_in:
-                group=group_in.dat,
-            #end if
-            #if $taxonomy_in:
-                taxonomy=taxonomy_in.dat,
-            #end if
-            #if $trim.method == "oligos":
-                oligos=trim.oligos.dat,
-                nomatch=$trim.nomatch,
-                $trim.keepprimer
-            #elif $trim.method == "reference":
-                ecoli=trim.ecoli.dat,
-            #elif $trim.method == "position":
-                start=$trim.start,
-                #if $trim.end and int($trim.end) > 0:
-                    end=$trim.end,
-                #end if
-            #end if
-            #if $pdiffs:
-                pdiffs=$pdiffs,
-            #end if
-            $keepdots
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'pcr.seqs(
+    fasta=fasta.dat,
+    #if $name_in
+        name=name_in.dat,
+    #end if
+    #if $group_in:
+        group=group_in.dat,
+    #end if
+    #if $taxonomy_in:
+        taxonomy=taxonomy_in.dat,
+    #end if
+    #if $trim.method == "oligos":
+        oligos=trim.oligos.dat,
+        nomatch=$trim.nomatch,
+        $trim.keepprimer
+    #elif $trim.method == "reference":
+        ecoli=trim.ecoli.dat,
+    #elif $trim.method == "position":
+        start=$trim.start,
+        #if $trim.end and int($trim.end) > 0:
+            end=$trim.end,
+        #end if
+    #end if
+    pdiffs=$pdiffs,
+    rdiffs=$rdiffs,
+    $keepdots
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
+        <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
         <conditional name="trim">
             <param name="method" type="select" label="Trim with an oligos file?" help="">
                 <option value="oligos">oligos</option>
@@ -81,12 +80,13 @@
         <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/>
         <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
         <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
-        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
+        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the forward primers (default 0)"/>
+        <param name="rdiffs" type="integer" value="0" min="0" label="rdiffs - number of differences to allow in the reverse primers (default 0)"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
-        <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
+        <data name="pcr_fasta" format_source="fasta" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
+        <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
         <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
             <filter>taxonomy_in</filter>
         </data>
@@ -116,7 +116,7 @@
             <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
             <param name="keepdots" value="keepdots=false,"/>
             <param name="method" value="reference"/>
-            <param name="ecoli" value="amazon.align_head"/>
+            <param name="ecoli" value="amazon.align_head" ftype="mothur.align"/>
             <param name="name_in" value="amazon.align_head.names"/>
             <param name="pdiffs" value="2"/>
             <expand macro="logfile-test"/>
@@ -142,8 +142,7 @@
             <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -153,7 +152,6 @@
 
 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>