--- a/freebayes.xml	Fri Aug 29 12:15:44 2014 -0400
+++ b/freebayes.xml	Tue Dec 16 16:15:43 2014 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="freebayes-0.9.14">
+<tool id="freebayes" name="FreeBayes" version="0.3">
   <requirements>
-    <requirement type="package" version="freebayes-0.9.14_8a407cf5f4">freebayes</requirement>
+    <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
-  <description> - Bayesian genetic variant detector</description>
+  <description> - bayesian genetic variant detector</description>
   <command>
     ##set up input files
 
@@ -24,9 +24,9 @@
     
     ## Tabixize optional input_varinat_vcf file (for --variant-input option)
     
-    #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-        ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" input_variant_vcf.vcf.gz &amp;&amp;
-        ln -s "${Tabixized_input}" input_variant_vcf.vcf.gz.tbi &amp;&amp;
+    #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and $options_type.optional_inputs.optional_inputs_selector and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+        ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &amp;&amp;
+        ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &amp;&amp;
     #end if
     
     ##finished setting up inputs
@@ -74,12 +74,14 @@
       --report-monomorphic
       --standard-filters
       --min-coverage "${options_type.min_coverage}"
-      
-    #elif str( $options_type.options_type_selector ) == "cline":
+
+##    Command line direct text entry is not allowed at this time for security reasons
+
+##    #elif str( $options_type.options_type_selector ) == "cline":
     
-      ${options_type.cline}
+##      ${options_type.cline}
   
-      @optional_inputs_outputs@
+##      @optional_inputs_outputs@
     
     #elif str( $options_type.options_type_selector ) == "full":
     
@@ -193,7 +195,7 @@
   
   <macros>
       <token name="@optional_inputs_outputs@">     
-      ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline"
+      ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline" ( cline is not supported at this time )
       
       #if $options_type.optional_inputs.optional_inputs_selector:
         
@@ -218,7 +220,7 @@
           #end if
           
           #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-            --variant-input input_variant_vcf.vcf.gz  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
+            --variant-input "input_variant_vcf.vcf.gz"  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
             ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
           #end if
           
@@ -282,13 +284,12 @@
         <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="1" message="Sequences are not currently available for the specified build." />
+              <validator type="dataset_metadata_in_data_table" table_name="fasta_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">
-          <options from_data_table="sam_fa_indexes">
-            <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
-          </options>
+          <options from_data_table="fasta_indexes"></options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
@@ -296,7 +297,7 @@
         <repeat name="input_bams" title="Sample BAM file" min="1">
           <param name="input_bam" type="data" format="bam" label="BAM file" />
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+        <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
       </when>
     </conditional>
     
@@ -326,7 +327,9 @@
         <option value="naive">3:Frequency-based pooled calling</option>
         <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
         <option value="full">5:Complete list of all options</option>
+        <!-- We will not alloow command line text boxes at this time
         <option value="cline">6:Input parameters on the command line</option>
+        -->
       </param>
       <when value="full">
    
@@ -503,9 +506,11 @@
     <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
     <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0  " />
   </when>
+  
+  <!-- We will not allow command line textboxes at this time
   <when value="cline">
     
-    <expand macro="optional_file_inputs" /> <!-- see macros section -->
+    <expand macro="optional_file_inputs" /> 
     
     <param name="cline" size="60" type="text" value="-m 20 -q 30" label="Type command line tags here" help="All paremeters that DO NOT involve filenames can be typed here. Use &quot;Do you want to provide additional inputs?&quot; section above to control input and output files. For full syntax check help section below">
       <sanitizer>
@@ -518,6 +523,7 @@
       </sanitizer>
     </param>
   </when>
+  -->
 
 </conditional>
 
@@ -550,7 +556,7 @@
 
 See https://github.com/ekg/freebayes for details on FreeBayes.
 
-This Galaxy instance of FreeBayes corresponds to release 8a407cf5f4416b5eba5bf27ca80144cd5e75bb80
+This Galaxy instance of FreeBayes corresponds to release 0.9.18
 
 ------
 
@@ -577,7 +583,6 @@
  3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes. 
  4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
  5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
- 6. *Input parameters on the command line*: Similar to the choice above but for those who does not like clicking. Here options can be directly typed into a text box.
 
 -----
 
@@ -836,4 +841,14 @@
 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
 
   </help>
+  
+  <citations>
+    <citation type="bibtex">@misc{1207.3907,
+Author = {Erik Garrison},
+Title = {Haplotype-based variant detection from short-read sequencing},
+Year = {2012},
+Eprint = {arXiv:1207.3907},
+url = {http://arxiv.org/abs/1207.3907},
+}</citation>
+  </citations>
 </tool>