--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira3/mira.xml	Thu Jan 30 13:21:21 2014 -0500
@@ -0,0 +1,191 @@
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
+    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
+    <requirements>
+        <requirement type="binary">mira</requirement>
+        <requirement type="package" version="3.4.1.1">MIRA</requirement>
+    </requirements>
+    <version_command interpreter="python">mira.py -v</version_command>
+    <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
+##Give the wrapper script list of output filenames, then the mira command...
+mira --job=$job_method,$job_type,$job_quality
+
+##Input files
+#if $condBackbone.use == "true":
+    ## Can this be linked to job_method as well? If mapping we need the backbone...
+    -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
+#end if
+#if $condSanger.use == "true":
+    SANGER_SETTINGS
+    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
+#end if
+#if $condRoche.use == "true":
+    454_SETTINGS
+    ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
+#end if
+#if $condIllumina.use == "true":
+    SOLEXA_SETTINGS
+    ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
+    ##TODO - Look at -LR FASTQ qual offset (fqqo)
+#end if
+#if $condIonTorrent.use == "true":
+    IONTOR_SETTINGS
+    ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
+#end if
+
+##Output files
+COMMON_SETTINGS
+
+##ignore warnings about long read names
+-MI:somrnl=0
+
+##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
+##Explicitly disable formats we won't use like MAF (reduce IO)
+-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
+
+##remove_rollover_tmps, remove_tmp_directory
+-OUT:rrot=1:rtd=1
+
+##put mira temp directory on local storage                                                                              
+-DI:trt=/tmp
+
+    </command>
+    <inputs>
+        <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
+            <option value="denovo">De novo</option>
+            <option value="mapping">Mapping</option>
+        </param>
+        <param name="job_type" type="select" label="Assembly type">
+            <option value="genome">Genome</option>
+            <option value="est">EST (transcriptome)</option>
+        </param>
+        <param name="job_quality" type="select" label="Assembly quality grade">
+            <option value="accurate">Accurate</option>
+            <option value="normal">Normal (deprecated)</option>
+            <option value="draft">Draft</option>
+        </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>
+        </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>
+        </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>
+        </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>
+        </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>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
+        <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
+        <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
+        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
+        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
+        <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
+        <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>
+-->
+    </tests>
+    <help>
+
+**What it does**
+
+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 Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, 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
+
+Bastien Chevreux, Thomas Wetter and Sándor Suhai (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.
+http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+    </help>
+</tool>