# HG changeset patch
# User soranzo
# Date 1392652436 18000
# Node ID e9ebed0c12f663595e900460ef4a2114e574ef48
# Parent  07d55d9ea9a42e9786cf78b10a21ae6c6d3c9ef2
Check exit code instead of stderr, since FreeBayes writes warnings there (e.g. "Could not find any mapped reads in target region chr1:955302..955952"). Also document change of available options in FreeBayes >= 0.9.9.

diff -r 07d55d9ea9a4 -r e9ebed0c12f6 freebayes.xml
--- a/freebayes.xml	Mon Dec 16 16:31:57 2013 -0500
+++ b/freebayes.xml	Mon Feb 17 10:53:56 2014 -0500
@@ -156,7 +156,6 @@
             --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}"
             ${options_type.section_algorithmic_features_type.no_marginals}
         #end if
-        
     #end if
   </command>
   <inputs>
@@ -169,7 +168,7 @@
         <repeat name="input_bams" title="Sample BAM file" min="1">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." />
+              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
             </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -307,7 +306,9 @@
         </conditional>
         
         <!-- indel realignment -->
-        <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" />
+        <!-- in FreeBayes < 0.9.9 the default is to not left-align indels and the available option is - -left-align-indels,
+             in FreeBayes >= 0.9.9 the default is to left-align indels and the available option is - -dont-left-align-indels -->
+        <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left align indels" />
         
         <!-- input filters -->
         <conditional name="section_input_filters_type">
@@ -429,6 +430,9 @@
       <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
     </test>
   </tests>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
   <help>
 **What it does**