--- a/cryptogenotyper.xml	Fri Oct 16 02:23:24 2020 +0000
+++ b/cryptogenotyper.xml	Fri Oct 16 22:32:56 2020 +0000
@@ -1,6 +1,6 @@
-<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@">
+<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
   <description>
-    CryptoGenotyper is a standalone tool to analyze Cryptosporidium Sanger sequencing data and classify the species and subtype based on SSU rRNA and gp60 gene markers, respectively.
+    classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
   </description>
   <macros>
    <token name="@VERSION@">1.0</token>
@@ -14,29 +14,27 @@
 
      #set $ref_file=''
 
-     #if $reference.ref == "no"
-        ln -s "${reference.db}" "${reference.db.name}" &&
-        #set $ref_file = $reference.db.name
+     #if $db
+        ln -s '${db}' '${db.name}' &&
+        #set $ref_file = $db.name
      #end if
 
-     #if $primers["seqtype"] == "contig"
-        ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" &&
-        ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" &&
-        cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse"
-        #if $reference.ref == "no"
+     #if $primers['seqtype'] == 'contig'
+        ln -s '${$primers.abi_input['forward']}' '${primers.abi_input.name}_forward.ab1' &&
+        ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' &&
+        cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
+        #if $db
           --databasefile $ref_file
         #end if
      #else
-        ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" &&
-        cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r ""
-        #if $reference.ref == "no"
+        ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' &&
+        cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype'
+        #if $db
           --databasefile $ref_file
         #end if
      #end if
-     #if $outputheader == "no"
-           --noheaderline
-     #end if
-     -o "result";
+     $outputheader
+     -o 'result'
      ]]>
   </command>
   <inputs>
@@ -44,17 +42,7 @@
           <option value="18S">SSU rRNA</option>
           <option value="gp60">gp60</option>
       </param>
-      <conditional name="reference">
-        <param name="ref" type="select" label="Use default reference file?">
-            <option value="yes">Yes</option>
-            <option value="no">No</option>
-        </param>
-        <when value="yes">
-        </when>
-        <when value="no">
-            <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/>
-        </when>
-      </conditional>
+      <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
       <conditional name="primers">
         <param name="seqtype" type="select" label="Type of Sequences">
             <option value="forward">Forward Only</option>
@@ -62,18 +50,16 @@
             <option selected="true" value="contig">Contig</option>
         </param>
         <when value="contig">
-          <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/>
+          <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/>
         </when>
         <when value="forward">
-          <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/>
+          <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/>
         </when>
         <when value="reverse">
-          <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/>
+          <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/>
         </when>
      </conditional>
-     <param name="outputheader" type="select" value="yes" label="Output header line in the report?">
-        <option value="yes">Yes</option>
-        <option value="no">No</option>
+     <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
      </param>
 
 
@@ -84,7 +70,7 @@
   </outputs>
 
   <tests>
-    <test>
+    <test expect_num_outputs="2">
       <param name="marker" value="18S"/>
       <param name="seqtype" value="forward"/>
       <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
@@ -94,7 +80,7 @@
           </assert_contents>
       </output>
     </test>
-    <test>
+    <test expect_num_outputs="2">
       <param name="marker" value="gp60"/>
       <param name="seqtype" value="forward"/>
       <param name="abi_input"  value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>