# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1345838421 14400
# Node ID 949ac66308a700006d64b555239cffe2e99374de
# Parent  e54bb199a47b078fc9b16345df982d46333ffa9b
Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.

diff -r e54bb199a47b -r 949ac66308a7 freebayes.xml
--- a/freebayes.xml	Wed Aug 15 10:43:46 2012 -0400
+++ b/freebayes.xml	Fri Aug 24 16:00:21 2012 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="0.0.2">
+<tool id="freebayes" name="FreeBayes" version="0.0.3">
   <requirements>
-    <requirement type="package" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">freebayes</requirement>
-    <requirement type="package" version="0.1.18">samtools</requirement>
+    <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
+    <requirement type="package">samtools</requirement>
   </requirements>
   <description> - Bayesian genetic variant detector</description>
   <command>
@@ -59,6 +59,10 @@
             --variant-input "${options_type.input_variant_type.input_variant_vcf}"
             ${options_type.input_variant_type.only_use_input_alleles}
         #end if
+        #if $options_type.haplotype_basis_alleles:
+            --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"
+        #end if
+        
         
         ##reporting
         #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
@@ -98,12 +102,12 @@
         ##input filters
         #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
             ${options_type.section_input_filters_type.use_duplicate_reads}
-            #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters":
-                --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}"
-                --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}"
-                --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}"
-            #else:
-                --no-filters
+            #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters":
+                --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}"
+                --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}"
+                --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}"
+            #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters":
+                --standard-filters
             #end if
             --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
             #if $options_type.section_input_filters_type.read_mismatch_limit:
@@ -233,7 +237,7 @@
             <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
           </when>
         </conditional>
-        
+        <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" />
         
         <!-- reporting -->
         <conditional name="section_reporting_type">
@@ -316,17 +320,17 @@
           </when>
           <when value="set">
             <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" />
-            <conditional name="no_filter_type">
-              <param name="no_filter_type_selector" type="select" label="Apply filters">
-                <option value="apply_filters" selected="True">Apply</option>
-                <option value="no_filters">Do not apply</option>
+            <conditional name="quality_filter_type">
+              <param name="quality_filter_type_selector" type="select" label="Apply Quality filters">
+                <option value="standard_filters" selected="True">Apply standard</option>
+                <option value="apply_filters">Apply specified</option>
               </param>
-              <when value="no_filters">
-                <!-- Do nothing here --> <!-- no-filters -->
+              <when value="standard_filters">
+                <!-- Do nothing here --> <!-- standard-filters -->
               </when>
               <when value="apply_filters">
-                <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" />
-                <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" />
+                <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="0" />
+                <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="0" />
                 <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" />
                 <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" />
               </when>
@@ -423,8 +427,6 @@
       <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/>
       <param name="options_type_selector" value="basic"/>
       <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
-      <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" />
-      <output name="output_trace" file="freebayes_out_1.output_trace" /> -->
     </test>
   </tests>
   <help>
@@ -494,6 +496,10 @@
                    and alleles which are provided in the VCF input, and provide
                    output in the VCF for all input alleles, not just those which
                    have support in the data.
+   --haplotype-basis-alleles VCF
+                   When specified, only variant alleles provided in this input
+                   VCF will be used for the construction of complex or haplotype
+                   alleles.
 
   reporting:
 
@@ -577,8 +583,8 @@
    -e --read-indel-limit N
                    Exclude reads with more than N separate gaps.
                    default: ~unbounded
-   -0 --no-filters Do not use any input base and mapping quality filters
-                   Equivalent to -m 0 -q 0 -R 0 -S 0
+   -0 --standard-filters  Use stringent input base and mapping quality filters
+                   Equivalent to -m 30 -q 20 -R 0 -S 0
    -x --indel-exclusion-window
                    Ignore portions of alignments this many bases from a
                    putative insertion or deletion allele.  default: 0
@@ -662,7 +668,7 @@
 
 **Citation**
 
-For the underlying tool, please cite `FreeBayes &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_.
+For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
 
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
diff -r e54bb199a47b -r 949ac66308a7 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Aug 15 10:43:46 2012 -0400
+++ b/tool_dependencies.xml	Fri Aug 24 16:00:21 2012 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="freebayes" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">
+    <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                <action type="shell_command">git reset --hard a46483351fd0196637614121868fb5c386612b55</action>
+                <action type="shell_command">git reset --hard 9608597d12e127c847ae03aa03440ab63992fedf</action>
                 <action type="shell_command">make</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>