--- a/tools/mira3/mira.xml	Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/mira.xml	Wed Apr 30 07:21:57 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.10">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -72,61 +72,61 @@
         </param>
         <!-- Backbone -->
         <conditional name="condBackbone">
-           <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
-              <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
-           </when>
+            <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
+                <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
+            </when>
         </conditional>
         <!-- Sanger -->
         <conditional name="condSanger">
-           <param name="use" type="select" label="Sanger/Capillary reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Sanger/Capillary reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Roche 454 -->
         <conditional name="condRoche">
-           <param name="use" type="select" label="454 reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
-              <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="454 reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
+                <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Illumina -->
         <conditional name="condIllumina">
-           <param name="use" type="select" label="Solexa/Illumina reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Solexa/Illumina reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Ion Torrent -->
         <conditional name="condIonTorrent">
-           <param name="use" type="select" label="Ion Torrent reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
-              <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Ion Torrent reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
+                <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
+            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -138,24 +138,25 @@
         <data name="out_log" format="txt" label="MIRA log" />
     </outputs>
     <tests>
-            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
-                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
-<!--
-Commenting out test until Galaxy framework is fixed,
-https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
+        <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
+             strain data and miraSearchESTSNPs. Here we just assemble it. --> 
         <test>
             <param name="job_method" value="denovo" />
             <param name="job_type" value="est" />
             <param name="job_qual" value="accurate" />
-            <param name="condBackbone.use" value="false" />
-            <param name="condSanger.use" value="true" />
-            <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
-            <param name="condRoche.use" value="false" />
-            <param name="condIllumina.use" value="false" /> 
-            <param name="condIonTorrent.use" value="false" />
+            <param name="condBackbone|use" value="false" />
+            <param name="condSanger|use" value="true" />
+            <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
+            <param name="condRoche|use" value="false" />
+            <param name="condIllumina|use" value="false" /> 
+            <param name="condIonTorrent|use" value="false" />
             <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
-	</test>
--->
+            <output name="out_qual" file="empty_file.dat" compare="contains" />
+            <output name="out_caf" file="empty_file.dat" compare="contains" />
+            <output name="out_ace" file="empty_file.dat" compare="contains" />
+            <output name="out_wig" file="empty_file.dat" compare="contains" />
+            <output name="out_log" file="empty_file.dat" compare="contains" />
+        </test>
     </tests>
     <help>