# HG changeset patch
# User devteam
# Date 1418764543 18000
# Node ID 6d94070200661eec4319f2ac3fb449be5ab1e36b
# Parent  59731e950e23398a0fdc435ec6ec0d46ccfc0c4b
Uploaded

diff -r 59731e950e23 -r 6d9407020066 freebayes.xml
--- 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>
diff -r 59731e950e23 -r 6d9407020066 leftalign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/leftalign.xml	Tue Dec 16 16:15:43 2014 -0500
@@ -0,0 +1,85 @@
+<?xml version="1.0"?>
+<tool id="bamleftalign" name="BamLeftAlign" version="0.3">
+  <requirements>
+    <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <description> indels in BAM datasets</description>
+  <command>
+    ##set up input files
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for leftalign" &gt;&amp;2 &amp;&amp;
+    #else:
+        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+
+    ##finished setting up inputs
+    
+    ##start leftalign commandline
+    samtools view -bh "${input_bam}" | bamleftalign
+    --fasta-reference "${reference_fasta_filename}"
+    -c
+    --max-iterations "${iterations}"
+    ##outputs
+    > "${output_bam}"
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+            <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign">
+              <validator type="unspecified_build" />
+              <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+            </param>
+        <param name="ref_file" type="select" label="Using reference genome">
+          <options from_data_table="fasta_indexes"></options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> 
+            <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+    <param name="iterations" type="integer" size="3" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" />
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" />
+  </outputs>
+  <tests>
+    <test>
+     <param name="reference_source_selector" value="history" />
+      <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
+      <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
+      <param name="iterations" value="5"/>
+      <output name="output_bam" file="left-align-output.bam" />
+    </test>
+  </tests>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <help>
+
+When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.
+
+This is leftalign utility from FreeBayes package developed and maintained by Erik Garrison (https://github.com/ekg/freebayes).
+  </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>
diff -r 59731e950e23 -r 6d9407020066 test-data/left-align-input.bam
Binary file test-data/left-align-input.bam has changed
diff -r 59731e950e23 -r 6d9407020066 test-data/left-align-output.bam
Binary file test-data/left-align-output.bam has changed
diff -r 59731e950e23 -r 6d9407020066 test-data/leftalign.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/leftalign.fa	Tue Dec 16 16:15:43 2014 -0500
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 59731e950e23 -r 6d9407020066 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Tue Dec 16 16:15:43 2014 -0500
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 59731e950e23 -r 6d9407020066 tool-data/sam_fa_indices.loc.sample
--- a/tool-data/sam_fa_indices.loc.sample	Fri Aug 29 12:15:44 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The sam_fa_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#index	<seq>	<location>
-#
-#So, for example, if you had hg18 indexed stored in 
-#/depot/data2/galaxy/sam/, 
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for 
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff -r 59731e950e23 -r 6d9407020066 tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample	Fri Aug 29 12:15:44 2014 -0400
+++ b/tool-data/tool_data_table_conf.xml.sample	Tue Dec 16 16:15:43 2014 -0500
@@ -1,8 +1,8 @@
 <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
     </table>
 </tables>
diff -r 59731e950e23 -r 6d9407020066 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 29 12:15:44 2014 -0400
+++ b/tool_dependencies.xml	Tue Dec 16 16:15:43 2014 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="freebayes" version="freebayes-0.9.14_8a407cf5f4">
-        <repository changeset_revision="77a97e5d2658" name="freebayes_0_9_14_8a407cf5f4" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="freebayes" version="0.9.18_0059bdf">
+        <repository changeset_revision="8f3ba7808a87" name="package_freebayes_0_9_18_0059bdf" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>