--- a/tools/mira4_0/mira4_mapping.xml	Fri Oct 02 06:12:23 2015 -0400
+++ b/tools/mira4_0/mira4_mapping.xml	Thu Aug 10 11:09:10 2017 -0400
@@ -1,28 +1,23 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.9">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.11">
     <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
-        <requirement type="binary">mira</requirement>
-        <requirement type="binary">miraconvert</requirement>
         <requirement type="package" version="4.0.2">MIRA</requirement>
-        <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">mira4.py --version</version_command>
-    <command interpreter="python">mira4.py
---manifest "$manifest"
+    <version_command>
+python $__tool_directory__/mira4.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/mira4.py
+--manifest '$manifest'
 #if str($maf_wanted) == "true":
---maf "$out_maf"
+--maf '$out_maf'
 #end if
 #if str($bam_wanted) == "true":
---bam "$out_bam"
+--bam '$out_bam'
 #end if
---fasta "$out_fasta"
---log "$out_log"
+--fasta '$out_fasta'
+--log '$out_log'
     </command>
     <configfiles>
         <configfile name="manifest">
@@ -121,7 +116,7 @@
         <!-- TODO? Allow strain settings for reference(s) and reads? -->
         <!-- TODO? Use a repeat to allow for multi-strain references? -->
         <!-- TODO? Add strain to the mapping read groups? -->
-        <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)"
+        <param name="references" type="data" format="fasta,fastq,mira" multiple="true" optional="false" label="Backbone reference file(s)"
                help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
         <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
             <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
@@ -158,11 +153,11 @@
                 </when>
                 <when value="none" /><!-- no further questions -->
             </conditional>
-            <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
+            <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" 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" />
+        <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)" />