--- a/tools/sr_assembly/mira.xml	Tue Jun 21 09:50:32 2011 -0400
+++ b/tools/sr_assembly/mira.xml	Wed Dec 21 11:33:19 2011 -0500
@@ -1,40 +1,46 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2">
-    <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
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3">
+    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
+	<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 $condBackbone.use == "true":
     ## Can this be linked to job_method as well? If mapping we need the backbone...
-    -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
+    -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename}
 #end if
 #if $condSanger.use == "true":
-    Sanger_SETTINGS
-    ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=yes
+    SANGER_SETTINGS
+    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
     ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
 #end if
 #if $condRoche.use == "true":
     454_SETTINGS
-    ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=yes
+    ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
     ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
+    -LR:lsd=1:mxti=0: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}
+    ## 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
-##remove_rollover_logs, remove_log_directory
--OUT:rrol=yes -OUT:rld=yes
+##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
 
     </command>
 	<inputs>
@@ -47,9 +53,9 @@
             <option value="est">EST (transcriptome)</option>
         </param>
         <param name="job_quality" type="select" label="Assembly quality grade">
-            <option value="normal">Normal</option>
+            <option value="accurate">Accurate</option>
+            <option value="normal">Normal (deprecated)</option>
             <option value="draft">Draft</option>
-            <option value="accurate">Accurate</option>
         </param>
         <!-- Backbone -->
         <conditional name="condBackbone">
@@ -82,7 +88,8 @@
            </param>
            <when value="false" />
            <when value="true">
-              <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" />
+              <!-- 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 -->
@@ -96,11 +103,22 @@
               <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_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)" />
@@ -117,9 +135,6 @@
 
 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