Mercurial > repos > devteam > freebayes

diff freebayes.xml @ 11:e9ebed0c12f6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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.
author soranzo
date Mon, 17 Feb 2014 10:53:56 -0500
parents fcb60273c710
children
line wrap: on
line diff
--- 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**