--- a/tools/mira4/mira4_de_novo.xml	Mon Oct 28 05:44:46 2013 -0400
+++ b/tools/mira4/mira4_de_novo.xml	Thu Nov 28 05:07:59 2013 -0500
@@ -1,13 +1,21 @@
-<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.2">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
+        <requirement type="binary">miraconvert</requirement>
         <requirement type="package" version="4.0">MIRA</requirement>
+        <requirement type="binary">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <version_command interpreter="python">mira4.py --version</version_command>
     <command interpreter="python">
-mira4.py $manifest $out_maf $out_fasta $out_log
+mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
     </command>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <inputs>
         <param name="job_type" type="select" label="Assembly type">
             <option value="genome">Genome</option>
@@ -63,6 +71,7 @@
     <code file="mira4_validator.py" />
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
+        <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" />
         <data name="out_maf" format="mira" label="MIRA de novo assembly" />
         <data name="out_log" format="txt" label="MIRA de novo log" />
     </outputs>
@@ -118,30 +127,47 @@
         </configfile>
     </configfiles>
     <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
+        <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755
+             Note we're using just one repeat group, and only the filenames parameter
+             within it, so this should work with current test framework limitations:
+        <test>
+            <param name="job_type" value="genome" />
+            <param name="job_quality" value="accurate" />
+            <param name="filenames" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
+            <output name="out_fasta" file="SRR639755_mito_pairs.mira4_de_novo.fasta" ftype="fasta" />
+        </test>
+        -->
+        <!-- Simple assembly based on MIRA's minidemo/demo4 example
+             Note we're using just one repeat group,
+             but several parameters with the repeat
+             (in order to specify sanger reads, no pairing)
         <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" />
-            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
-	</test>
--->
+            <param name="job_type" value="genome" />
+            <param name="job_quality" value="accurate" />
+            <param name="technology" value="sanger" />
+            <param name="type" value="none" />
+            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
+            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
+        </test>
+        -->
+	<!-- Simple assembly based on MIRA's minidemo/solexa1 example
+             Note we're using just one repeat group,
+             but two parameters within the repeat (filename, no pairing)
+        <test>
+            <param name="job_type" value="genome" />
+            <param name="job_quality" value="accurate" />
+            <param name="type" value="none" />
+            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
+            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
+        </test>
+        -->
     </tests>
     <help>
 
 **What it does**
 
-Runs MIRA v4.0 in de novo mode, collects the output, and throws away all the temporary files.
+Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM
+file, and then throws away all the temporary files.
 
 MIRA is an open source assembly tool capable of handling sequence data from
 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent