--- a/tools/mira4/mira4_mapping.xml	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/mira4_mapping.xml	Tue Jun 10 10:11:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.3">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.4">
     <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -8,8 +8,16 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <version_command interpreter="python">mira4.py --version</version_command>
-    <command interpreter="python">
-mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
+    <command interpreter="python">mira4.py
+--manifest "$manifest"
+#if str($maf_wanted) == "true":
+--maf "$out_maf"
+#end if
+#if str($bam_wanted) == "true":
+--bam "$out_bam"
+#end if
+--fasta "$out_fasta"
+--log "$out_log"
     </command>
     <stdio>
         <!-- Assume anything other than zero is an error -->
@@ -69,11 +77,17 @@
             <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
                    help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
+        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" />
+        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" />
     </inputs>
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
-        <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)" />
-        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
+        <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)">
+            <filter>bam_wanted is True</filter>
+        </data>
+        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly">
+            <filter>maf_wanted is True</filter>
+        </data>
         <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
     </outputs>
     <configfiles>
@@ -168,6 +182,8 @@
             <param name="strain_setup" value="default" />
             <param name="type" value="none" />
             <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />
@@ -180,6 +196,8 @@
             <param name="strain_setup" value="same" />
             <param name="type" value="none" />
             <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />