--- a/chimera.ccode.xml	Tue Sep 05 16:37:48 2017 -0400
+++ b/chimera.ccode.xml	Wed Feb 14 09:25:22 2018 -0500
@@ -7,107 +7,107 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$alignment.template" alignment.template.dat &&
-        #if $mask.source2 == "history":
-            ln -s "$mask.input" mask.input.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$alignment.reference' alignment.template.dat &&
+#if $mask_cond.source2 == "history":
+    ln -s '$mask_cond.input' mask_cond.mask.dat &&
+#end if
 
-        echo 'chimera.ccode(
-            fasta=fasta.dat,
-            reference=alignment.template.dat,
-            filter=$filter,
-            #if $mask.source2 == "default":
-                mask=default,
-            #elif $mask.source2 == "history":
-                mask=mask.input.dat,
-            #end if
-            #if int($window) > 0:
-                window=$window,
-            #end if
-            #if int($numwanted) > 0:
-                numwanted=$numwanted,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chimera.ccode(
+    fasta=fasta.dat,
+    reference=alignment.template.dat,
+    filter=$filter,
+    #if $mask_cond.source2 == "default":
+        mask=default,
+    #elif $mask_cond.source2 == "history":
+        mask=mask_cond.mask.dat,
+    #end if
+    #if int($window) > 0:
+        window=$window,
+    #end if
+    #if int($numwanted) > 0:
+        numwanted=$numwanted,
+    #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="mothur.align" label="fasta - Candiate Aligned Sequences"/>
+        <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
         <conditional name="alignment">
-            <param name="source" type="select" label="Select Reference Template from" help="">
+            <param name="source" type="select" label="Select Reference Template from">
                 <option value="hist">History</option>
                 <option value="ref">Cached Reference</option>
             </param>
             <when value="ref">
-                <param name="template" type="select" label="reference - Select an alignment database" help="">
-                    <options from_data_table="mothur_aligndb">
-                    </options>
+                <param argument="reference" type="select" label="reference - Select an alignment database">
+                    <options from_data_table="mothur_aligndb"/>
                 </param>
             </when>
             <when value="hist">
-                <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
             </when>
         </conditional>
-        <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
-        <conditional name="mask">
+        <param argument="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
+        <conditional name="mask_cond">
             <param name="source2" type="select" label="Mask option">
                 <option value="">None</option>
                 <option value="default">default ecoli mask</option>
                 <option value="history">From Your History</option>
             </param>
             <when value="history">
-                <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/>
+                <param argument="mask" type="data" format="mothur.filter" label="Mask for the reference file"/>
             </when>
             <when value=""/>
             <when value="default"/>
         </conditional>
-        <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
-        <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
+        <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed"
+            help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length. Default is used if &lt; 1"/>
+        <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query"
+            help="uses default if set to 0"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
-        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
+        <data name="ccode.chimeras" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
+        <data name="ccode.accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
         <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
     </outputs>
     <tests>
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <param name="source" value="hist"/>
-            <param name="template" value="HMP_MOCK.v35.align"/>
-            <output name="out_file" ftype="txt">
+            <param name="reference" value="HMP_MOCK.v35.align"/>
+            <output name="ccode.chimeras" ftype="txt">
                 <assert_contents>
                     <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
                 </assert_contents>
             </output>
-            <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
+            <output name="ccode.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
             <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
             <expand macro="logfile-test"/>
         </test>
         <test> <!-- test with default ecoli mask -->
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <param name="source" value="hist"/>
-            <param name="template" value="HMP_MOCK.v35.align"/>
+            <param name="reference" value="HMP_MOCK.v35.align"/>
             <param name="source2" value="default"/>
             <param name="window" value="100"/>
-            <output name="out_file" ftype="txt">
+            <output name="ccode.chimeras" ftype="txt">
                 <assert_contents>
                     <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
                 </assert_contents>
             </output>
-            <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
+            <output name="ccode.accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
             <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -123,7 +123,6 @@
 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
 .. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>