--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_assembly/mira.xml	Tue Jun 07 16:23:51 2011 -0400
@@ -0,0 +1,131 @@
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.1">
+    <description>Takes Sanger, Roche, and Illumina data</description>
+	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $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 $condBackbone.use == "true":
+    ## Can this be linked to job_method as well? If mapping we need the backbone...
+    -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
+#end if
+#if $condSanger.use == "true":
+    Sanger_SETTINGS
+    ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
+#end if
+#if $condRoche.use == "true":
+    454_SETTINGS
+    ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
+#end if
+#if $condIllumina.use == "true":
+    SOLEXA_SETTINGS
+    ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename}
+    ##TODO - Look at -LR FASTQ qual offset (fqqo)
+#end if
+
+
+##Output files
+COMMON_SETTINGS
+##remove_rollover_logs, remove_log_directory
+-OUT:rrol=yes -OUT:rld=yes
+
+    </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="normal">Normal</option>
+            <option value="draft">Draft</option>
+            <option value="accurate">Accurate</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">
+              <param name="filename" type="data" format="fastq,sff" 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>
+	</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_tcs" format="tabular" label="MIRA contigs summary" />
+	    <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>
+	</requirements>
+	<help>
+
+**What it does**
+
+Runs MIRA v3, collects the output, and throws away all the temporary files.
+
+The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy.
+This records one line per base per contig, and including things like the base, quality, coverage and any tags.
+
+**Citation**
+
+This tool uses MIRA. 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>