--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.xml	Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,155 @@
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
+    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
+	<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>
+	</tests>
+	<requirements>
+		<requirement type="python-module">Bio</requirement>
+		<requirement type="binary">mira</requirement>
+	</requirements>
+	<help>
+
+**What it does**
+
+Runs MIRA v3.4, collects the output, and throws away all the temporary files.
+
+**Citation**
+
+If you use this tool in scientific work leading to a publication, please cite:
+
+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.
+
+	</help>
+</tool>