--- a/tools/mira_3_4/mira.xml	Thu May 02 12:40:04 2013 -0400
+++ b/tools/mira_3_4/mira.xml	Wed Sep 11 06:21:44 2013 -0400
@@ -139,9 +139,12 @@
         <data name="out_log" format="txt" label="MIRA log" />
     </outputs>
     <tests>
-        <test>
             <!-- 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
+        <test>
             <param name="job_method" value="denovo" />
             <param name="job_type" value="est" />
             <param name="job_qual" value="accurate" />
@@ -153,6 +156,7 @@
             <param name="condIonTorrent.use" value="false" />
             <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
 	</test>
+-->
     </tests>
     <help>
 
@@ -160,14 +164,28 @@
 
 Runs MIRA v3.4, collects the output, and 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 and also
+Ion Torrent).
+
+It is particularly suited to small genomes such as bacteria.
+
 **Citation**
 
-If you use this tool in scientific work leading to a publication, please cite:
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
 
-Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Chevreux et al. (1999).
+Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
+Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
 
     </help>
 </tool>