diff tools/mira4/mira4_mapping.xml @ 9:302d13490b23 draft

Uploaded v0.0.2 preview 1, BAM output

--- a/tools/mira4/mira4_mapping.xml	Mon Oct 28 05:44:46 2013 -0400
+++ b/tools/mira4/mira4_mapping.xml	Thu Nov 28 05:07:59 2013 -0500
@@ -1,13 +1,21 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.1">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.2">
     <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">MIRA</requirement>
+        <requirement type="binary">samtools</requirement>
+        <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_fasta $out_log
+mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
     </command>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <inputs>
         <param name="job_type" type="select" label="Assembly type">
             <option value="genome">Genome</option>
@@ -64,6 +72,7 @@
     </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($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
         <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
     </outputs>
@@ -169,7 +178,8 @@
 
 **What it does**
 
-Runs MIRA v4.0 in mapping mode, collects the output, and throws away all the temporary files.
+Runs MIRA v4.0 in mapping mode, collects the output, generates a sorted BAM
+file, and throws away all the temporary files.
 
 MIRA is an open source assembly tool capable of handling sequence data from
 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent