changeset 1:30e1dd77e99c draft default tip

Uploaded correct tarball.
author devteam
date Mon, 14 Apr 2014 08:48:25 -0400
parents 53dd1bfced54
children
files table_recalibration.xml test-data/1.bam test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains test-data/phiX.fasta tool-data/gatk_annotations.txt.sample tool_data_table_conf.xml.sample tool_dependencies.xml variant_recalibrator.xml
diffstat 11 files changed, 578 insertions(+), 468 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/table_recalibration.xml	Mon Apr 14 08:48:25 2014 -0400
@@ -0,0 +1,232 @@
+<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.5">
+  <description>on BAM files</description>
+  <requirements>
+      <requirement type="package" version="1.4">gatk</requirement>
+      <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <macros>
+    <import>gatk_macros.xml</import>
+  </macros>
+  <command interpreter="python">gatk_wrapper.py
+   --max_jvm_heap_fraction "1"
+   --stdout "${output_log}"
+   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+   #end if
+   -p 'java 
+    -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
+    -T "TableRecalibration"
+    -o "${output_bam}"
+    -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
+    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    --recal_file "${input_recal}"
+    --disable_bam_indexing
+   '
+    #include source=$standard_gatk_options#
+    
+    ##start analysis specific options
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        -p '
+        #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
+            --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
+        #end if
+        #if str( $analysis_param_type.default_platform ) != "default":
+            --default_platform "${analysis_param_type.default_platform}"
+        #end if
+        #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
+            --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
+        #end if
+        #if str( $analysis_param_type.force_platform ) != "default":
+            --force_platform "${analysis_param_type.force_platform}"
+        #end if
+        ${analysis_param_type.exception_if_no_tile}
+        #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
+            #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
+                --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 
+            #end if
+            #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
+                --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 
+            #end if
+        #end if
+        ${analysis_param_type.simplify_bam}
+        --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
+        --smoothing "${analysis_param_type.smoothing}"
+        --max_quality_score "${analysis_param_type.max_quality_score}"
+        --window_size_nqs "${analysis_param_type.window_size_nqs}"
+        --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
+        ${analysis_param_type.do_not_write_original_quals}
+        '
+    #end if
+  </command>
+  <inputs>
+    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
+    <conditional name="reference_source">
+      <expand macro="reference_source_selector_param" />
+      <when value="cached">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
+          <validator type="unspecified_build" />
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+        </param>
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
+          <options from_data_table="gatk_picard_indexes">
+            <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
+          </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 file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options>
+            <filter type="data_meta" key="dbkey" ref="input_bam" />
+          </options>
+        </param>
+      </when>
+    </conditional>
+    
+    <expand macro="gatk_param_type_conditional" />
+    
+    
+    <expand macro="analysis_type_conditional">
+        <conditional name="default_read_group_type">
+          <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
+            <option value="default" selected="True">Don't Set</option>
+            <option value="set">Set</option>
+          </param>
+          <when value="default">
+            <!-- do nothing here -->
+          </when>
+          <when value="set">
+            <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
+          </when>
+        </conditional>
+        <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
+          <option value="default" selected="True">Don't Set</option>
+          <option value="illumina">illumina</option>
+          <option value="454">454</option>
+          <option value="solid">solid</option>
+        </param>
+        <conditional name="force_read_group_type">
+          <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
+            <option value="default" selected="True">Don't Force</option>
+            <option value="set">Force</option>
+          </param>
+          <when value="default">
+            <!-- do nothing here -->
+          </when>
+          <when value="set">
+            <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
+          </when>
+        </conditional>
+        <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
+          <option value="default" selected="True">Don't Force</option>
+          <option value="illumina">illumina</option>
+          <option value="454">454</option>
+          <option value="solid">solid</option>
+        </param>
+        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
+        <conditional name="solid_options_type">
+          <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
+            <option value="default" selected="True">Don't Set</option>
+            <option value="set">Set</option>
+          </param>
+          <when value="default">
+            <!-- do nothing here -->
+          </when>
+          <when value="set">
+            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
+              <option value="default" selected="True">Don't set</option>
+              <option value="DO_NOTHING">DO_NOTHING</option>
+              <option value="SET_Q_ZERO">SET_Q_ZERO</option>
+              <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
+              <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
+            </param>
+            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
+              <option value="default" selected="True">Don't set</option>
+              <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
+              <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
+              <option value="PURGE_READ">PURGE_READ</option>
+            </param>
+          </when>
+        </conditional>
+        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
+        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
+        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
+        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
+        <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
+        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
+        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="basic" />
+          <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" />
+          <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.  For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads.  Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
+
+For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration&gt;`_.
+
+To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
+
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files.
+
+
+**Outputs**
+
+The output is in BAM format.
+
+
+Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ default_read_group             If a read has no read group then default to the provided String.
+ default_platform               If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
+ force_read_group               If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
+ force_platform                 If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
+ window_size_nqs                The window size used by MinimumNQSCovariate for its calculation
+ homopolymer_nback              The number of previous bases to look at in HomopolymerCovariate
+ exception_if_no_tile           If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
+ solid_recal_mode               How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
+ solid_nocall_strategy          Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
+ recal_file                     Filename for the input covariates table recalibration .csv file
+ out                            The output BAM file
+ bam_compression                Compression level to use for writing BAM files
+ disable_bam_indexing           Turn off on-the-fly creation of indices for output BAM files.
+ simplifyBAM                    If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
+ preserve_qscores_less_than     Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below &lt; 5, since base callers use these values to indicate random or bad bases
+ smoothing                      Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
+ max_quality_score              The integer value at which to cap the quality scores, default=50
+ doNotWriteOriginalQuals        If true, we will not write the original quality (OQ) tag for each read
+
+@CITATION_SECTION@
+  </help>
+</tool>
Binary file test-data/1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv	Mon Apr 14 08:48:25 2014 -0400
@@ -0,0 +1,246 @@
+# Counted Sites    41
+# Counted Bases    340
+# Skipped Sites    2
+# Fraction Skipped 1 / 21 bp
+ReadGroup,QualityScore,Cycle,Dinuc,Homopolymer,MinimumNQS,Position,nObservations,nMismatches,Qempirical
+A Fake phiX Sample,26,1,NN,0,26,0,9,0,40
+A Fake phiX Sample,26,1,NN,1,26,0,1,0,40
+A Fake phiX Sample,26,2,AG,0,26,1,1,0,40
+A Fake phiX Sample,26,2,CC,0,26,1,1,0,40
+A Fake phiX Sample,26,2,CG,0,26,1,3,0,40
+A Fake phiX Sample,26,2,GC,0,26,1,2,0,40
+A Fake phiX Sample,26,2,GC,1,26,1,1,0,40
+A Fake phiX Sample,26,2,GT,0,26,1,1,0,40
+A Fake phiX Sample,26,2,TG,1,26,1,1,0,40
+A Fake phiX Sample,26,3,CC,0,26,2,1,0,40
+A Fake phiX Sample,26,3,CG,0,26,2,3,0,40
+A Fake phiX Sample,26,3,GC,0,26,2,1,0,40
+A Fake phiX Sample,26,3,GC,1,26,2,2,0,40
+A Fake phiX Sample,26,3,GG,0,26,2,1,0,40
+A Fake phiX Sample,26,3,GT,0,26,2,1,0,40
+A Fake phiX Sample,26,3,TG,1,26,2,1,0,40
+A Fake phiX Sample,26,4,CC,0,26,3,2,0,40
+A Fake phiX Sample,26,4,CG,0,26,3,2,0,40
+A Fake phiX Sample,26,4,GA,0,26,3,1,0,40
+A Fake phiX Sample,26,4,GC,1,26,3,2,0,40
+A Fake phiX Sample,26,4,GG,0,26,3,1,0,40
+A Fake phiX Sample,26,4,GT,0,26,3,1,0,40
+A Fake phiX Sample,26,4,TG,1,26,3,1,0,40
+A Fake phiX Sample,26,5,AT,0,26,4,1,0,40
+A Fake phiX Sample,26,5,CC,0,26,4,2,0,40
+A Fake phiX Sample,26,5,CG,0,26,4,2,0,40
+A Fake phiX Sample,26,5,GA,0,26,4,1,0,40
+A Fake phiX Sample,26,5,GC,1,26,4,1,0,40
+A Fake phiX Sample,26,5,GG,0,26,4,1,0,40
+A Fake phiX Sample,26,5,GT,0,26,4,1,0,40
+A Fake phiX Sample,26,5,TG,1,26,4,1,0,40
+A Fake phiX Sample,26,6,AT,0,26,5,1,0,40
+A Fake phiX Sample,26,6,CC,0,26,5,1,0,40
+A Fake phiX Sample,26,6,CG,0,26,5,2,0,40
+A Fake phiX Sample,26,6,GA,0,26,5,1,0,40
+A Fake phiX Sample,26,6,GG,0,26,5,1,0,40
+A Fake phiX Sample,26,6,GT,0,26,5,2,0,40
+A Fake phiX Sample,26,6,TG,0,26,5,1,0,40
+A Fake phiX Sample,26,6,TG,1,26,5,1,0,40
+A Fake phiX Sample,26,7,AT,0,26,6,1,0,40
+A Fake phiX Sample,26,7,CG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,GA,0,26,6,2,1,3
+A Fake phiX Sample,26,7,GG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,GT,0,26,6,2,0,40
+A Fake phiX Sample,26,7,TG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,TG,1,26,6,2,0,40
+A Fake phiX Sample,26,8,AC,0,26,7,1,0,40
+A Fake phiX Sample,26,8,AT,0,26,7,1,0,40
+A Fake phiX Sample,26,8,GA,0,26,7,2,1,3
+A Fake phiX Sample,26,8,GG,0,26,7,2,0,40
+A Fake phiX Sample,26,8,GT,0,26,7,1,0,40
+A Fake phiX Sample,26,8,TG,0,26,7,1,0,40
+A Fake phiX Sample,26,8,TG,1,26,7,2,0,40
+A Fake phiX Sample,26,9,AC,0,26,8,1,0,40
+A Fake phiX Sample,26,9,AT,0,26,8,1,0,40
+A Fake phiX Sample,26,9,CT,0,26,8,1,0,40
+A Fake phiX Sample,26,9,GA,0,26,8,3,1,5
+A Fake phiX Sample,26,9,GG,0,26,8,2,0,40
+A Fake phiX Sample,26,9,TG,0,26,8,1,0,40
+A Fake phiX Sample,26,9,TG,1,26,8,1,0,40
+A Fake phiX Sample,26,10,AC,0,26,9,1,0,40
+A Fake phiX Sample,26,10,AT,0,26,9,2,0,40
+A Fake phiX Sample,26,10,CT,0,26,9,1,0,40
+A Fake phiX Sample,26,10,GA,0,26,9,3,1,5
+A Fake phiX Sample,26,10,GG,0,26,9,1,0,40
+A Fake phiX Sample,26,10,TG,0,26,9,2,0,40
+A Fake phiX Sample,26,11,AC,0,26,10,1,0,40
+A Fake phiX Sample,26,11,AT,0,26,10,2,0,40
+A Fake phiX Sample,26,11,CT,0,26,10,1,0,40
+A Fake phiX Sample,26,11,GA,0,26,10,3,1,5
+A Fake phiX Sample,26,11,TG,0,26,10,3,0,40
+A Fake phiX Sample,26,12,AC,0,26,11,1,0,40
+A Fake phiX Sample,26,12,AC,1,26,11,1,0,40
+A Fake phiX Sample,26,12,AT,0,26,11,1,0,40
+A Fake phiX Sample,26,12,CT,0,26,11,1,0,40
+A Fake phiX Sample,26,12,GA,0,26,11,2,1,3
+A Fake phiX Sample,26,12,GC,1,26,11,1,0,40
+A Fake phiX Sample,26,12,TG,0,26,11,3,0,40
+A Fake phiX Sample,26,13,AC,0,26,12,1,0,40
+A Fake phiX Sample,26,13,AC,1,26,12,1,0,40
+A Fake phiX Sample,26,13,CC,0,26,12,2,0,40
+A Fake phiX Sample,26,13,CT,0,26,12,1,0,40
+A Fake phiX Sample,26,13,GA,0,26,12,2,1,3
+A Fake phiX Sample,26,13,GC,1,26,12,1,0,40
+A Fake phiX Sample,26,13,TG,0,26,12,2,0,40
+A Fake phiX Sample,26,14,AC,0,26,13,1,0,40
+A Fake phiX Sample,26,14,AC,1,26,13,1,0,40
+A Fake phiX Sample,26,14,CC,0,26,13,2,0,40
+A Fake phiX Sample,26,14,CG,0,26,13,1,0,40
+A Fake phiX Sample,26,14,CT,0,26,13,2,0,40
+A Fake phiX Sample,26,14,GA,0,26,13,1,0,40
+A Fake phiX Sample,26,14,GC,1,26,13,1,0,40
+A Fake phiX Sample,26,14,TG,0,26,13,1,0,40
+A Fake phiX Sample,26,15,AC,1,26,14,1,0,40
+A Fake phiX Sample,26,15,CC,0,26,14,2,0,40
+A Fake phiX Sample,26,15,CG,0,26,14,1,0,40
+A Fake phiX Sample,26,15,CT,0,26,14,2,0,40
+A Fake phiX Sample,26,15,GA,0,26,14,1,0,40
+A Fake phiX Sample,26,15,GT,0,26,14,1,0,40
+A Fake phiX Sample,26,15,TG,0,26,14,2,0,40
+A Fake phiX Sample,26,16,AC,1,26,15,1,0,40
+A Fake phiX Sample,26,16,CC,0,26,15,1,0,40
+A Fake phiX Sample,26,16,CG,0,26,15,1,0,40
+A Fake phiX Sample,26,16,CT,0,26,15,1,0,40
+A Fake phiX Sample,26,16,GA,0,26,15,2,0,40
+A Fake phiX Sample,26,16,GT,0,26,15,1,0,40
+A Fake phiX Sample,26,16,TA,0,26,15,1,0,40
+A Fake phiX Sample,26,16,TG,0,26,15,2,0,40
+A Fake phiX Sample,26,17,AC,1,26,16,3,0,40
+A Fake phiX Sample,26,17,CC,0,26,16,1,0,40
+A Fake phiX Sample,26,17,CG,0,26,16,1,0,40
+A Fake phiX Sample,26,17,GA,0,26,16,2,0,40
+A Fake phiX Sample,26,17,GT,0,26,16,1,0,40
+A Fake phiX Sample,26,17,TA,0,26,16,1,0,40
+A Fake phiX Sample,26,17,TG,0,26,16,1,0,40
+A Fake phiX Sample,26,18,AC,1,26,17,3,0,40
+A Fake phiX Sample,26,18,CC,0,26,17,3,0,40
+A Fake phiX Sample,26,18,CG,0,26,17,1,0,40
+A Fake phiX Sample,26,18,GA,0,26,17,1,0,40
+A Fake phiX Sample,26,18,GT,0,26,17,1,0,40
+A Fake phiX Sample,26,18,TA,0,26,17,1,0,40
+A Fake phiX Sample,26,19,AC,1,26,18,2,0,40
+A Fake phiX Sample,26,19,CC,0,26,18,3,0,40
+A Fake phiX Sample,26,19,CG,0,26,18,3,0,40
+A Fake phiX Sample,26,19,GT,0,26,18,1,0,40
+A Fake phiX Sample,26,19,TA,0,26,18,1,0,40
+A Fake phiX Sample,26,20,AC,1,26,19,1,0,40
+A Fake phiX Sample,26,20,CC,0,26,19,2,0,40
+A Fake phiX Sample,26,20,CG,0,26,19,3,0,40
+A Fake phiX Sample,26,20,GA,0,26,19,1,0,40
+A Fake phiX Sample,26,20,GT,0,26,19,2,0,40
+A Fake phiX Sample,26,20,TA,0,26,19,1,0,40
+A Fake phiX Sample,26,21,AC,1,26,20,1,0,40
+A Fake phiX Sample,26,21,AG,1,26,20,1,0,40
+A Fake phiX Sample,26,21,CC,0,26,20,1,0,40
+A Fake phiX Sample,26,21,CG,0,26,20,2,0,40
+A Fake phiX Sample,26,21,GA,0,26,20,1,0,40
+A Fake phiX Sample,26,21,GT,0,26,20,2,0,40
+A Fake phiX Sample,26,21,TA,0,26,20,2,0,40
+A Fake phiX Sample,26,22,AC,1,26,21,2,0,40
+A Fake phiX Sample,26,22,AG,1,26,21,1,0,40
+A Fake phiX Sample,26,22,CC,0,26,21,1,0,40
+A Fake phiX Sample,26,22,CG,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GA,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GG,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GT,0,26,21,1,0,40
+A Fake phiX Sample,26,22,TA,0,26,21,2,0,40
+A Fake phiX Sample,26,23,AC,1,26,22,2,0,40
+A Fake phiX Sample,26,23,AG,1,26,22,1,0,40
+A Fake phiX Sample,26,23,CC,0,26,22,2,0,40
+A Fake phiX Sample,26,23,CG,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GA,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GC,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GG,0,26,22,1,0,40
+A Fake phiX Sample,26,23,TA,0,26,22,1,0,40
+A Fake phiX Sample,26,24,AC,1,26,23,1,0,40
+A Fake phiX Sample,26,24,AG,1,26,23,1,0,40
+A Fake phiX Sample,26,24,CC,0,26,23,2,0,40
+A Fake phiX Sample,26,24,CG,0,26,23,2,0,40
+A Fake phiX Sample,26,24,CT,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GA,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GC,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GG,0,26,23,1,0,40
+A Fake phiX Sample,26,25,AG,1,26,24,1,0,40
+A Fake phiX Sample,26,25,CC,0,26,24,1,0,40
+A Fake phiX Sample,26,25,CG,0,26,24,2,0,40
+A Fake phiX Sample,26,25,CT,0,26,24,1,0,40
+A Fake phiX Sample,26,25,GA,0,26,24,2,0,40
+A Fake phiX Sample,26,25,GC,0,26,24,1,0,40
+A Fake phiX Sample,26,25,GG,0,26,24,1,0,40
+A Fake phiX Sample,26,25,TA,1,26,24,1,0,40
+A Fake phiX Sample,26,26,AG,1,26,25,2,0,40
+A Fake phiX Sample,26,26,CG,0,26,25,1,0,40
+A Fake phiX Sample,26,26,CT,0,26,25,1,0,40
+A Fake phiX Sample,26,26,GA,0,26,25,2,0,40
+A Fake phiX Sample,26,26,GC,0,26,25,1,0,40
+A Fake phiX Sample,26,26,GG,0,26,25,1,0,40
+A Fake phiX Sample,26,26,TA,1,26,25,1,0,40
+A Fake phiX Sample,26,27,AC,2,26,26,1,0,40
+A Fake phiX Sample,26,27,AG,1,26,26,2,0,40
+A Fake phiX Sample,26,27,CT,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GA,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GC,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GG,0,26,26,2,0,40
+A Fake phiX Sample,26,27,TA,1,26,26,1,0,40
+A Fake phiX Sample,26,28,AC,2,26,27,1,0,40
+A Fake phiX Sample,26,28,AG,1,26,27,1,0,40
+A Fake phiX Sample,26,28,CC,1,26,27,1,0,40
+A Fake phiX Sample,26,28,CT,0,26,27,1,0,40
+A Fake phiX Sample,26,28,GC,0,26,27,2,0,40
+A Fake phiX Sample,26,28,GG,0,26,27,2,0,40
+A Fake phiX Sample,26,28,TA,1,26,27,1,0,40
+A Fake phiX Sample,26,29,AC,2,26,28,1,0,40
+A Fake phiX Sample,26,29,CC,1,26,28,1,0,40
+A Fake phiX Sample,26,29,CT,0,26,28,2,0,40
+A Fake phiX Sample,26,29,GC,0,26,28,2,0,40
+A Fake phiX Sample,26,29,GG,0,26,28,1,0,40
+A Fake phiX Sample,26,29,TA,1,26,28,1,0,40
+A Fake phiX Sample,26,30,AC,2,26,29,1,0,40
+A Fake phiX Sample,26,30,CC,1,26,29,1,0,40
+A Fake phiX Sample,26,30,CT,0,26,29,3,0,40
+A Fake phiX Sample,26,30,GC,0,26,29,1,0,40
+A Fake phiX Sample,26,30,TA,1,26,29,2,0,40
+A Fake phiX Sample,26,31,AC,2,26,30,1,0,40
+A Fake phiX Sample,26,31,CC,1,26,30,1,0,40
+A Fake phiX Sample,26,31,CT,0,26,30,2,0,40
+A Fake phiX Sample,26,31,TA,1,26,30,3,0,40
+A Fake phiX Sample,26,32,AA,0,26,31,1,0,40
+A Fake phiX Sample,26,32,AC,1,26,31,1,0,40
+A Fake phiX Sample,26,32,AC,2,26,31,1,0,40
+A Fake phiX Sample,26,32,CC,1,26,31,1,0,40
+A Fake phiX Sample,26,32,CT,0,26,31,1,0,40
+A Fake phiX Sample,26,32,TA,1,26,31,2,0,40
+A Fake phiX Sample,26,33,AA,0,26,32,1,0,40
+A Fake phiX Sample,26,33,AC,1,26,32,1,0,40
+A Fake phiX Sample,26,33,AC,2,26,32,1,0,40
+A Fake phiX Sample,26,33,AT,0,26,32,1,0,40
+A Fake phiX Sample,26,33,CC,1,26,32,1,0,40
+A Fake phiX Sample,26,33,CT,0,26,32,1,0,40
+A Fake phiX Sample,26,33,TA,1,26,32,1,0,40
+A Fake phiX Sample,26,34,AA,0,26,33,1,0,40
+A Fake phiX Sample,26,34,AC,1,26,33,1,0,40
+A Fake phiX Sample,26,34,AT,0,26,33,1,0,40
+A Fake phiX Sample,26,34,CC,1,26,33,1,0,40
+A Fake phiX Sample,26,34,CT,0,26,33,2,0,40
+A Fake phiX Sample,26,34,TA,1,26,33,1,0,40
+A Fake phiX Sample,26,34,TG,0,26,33,1,0,40
+A Fake phiX Sample,26,35,AA,0,26,34,1,0,40
+A Fake phiX Sample,26,35,AT,0,26,34,1,0,40
+A Fake phiX Sample,26,35,CT,0,26,34,2,0,40
+A Fake phiX Sample,26,35,GA,0,26,34,1,0,40
+A Fake phiX Sample,26,35,TA,1,26,34,2,0,40
+A Fake phiX Sample,26,35,TG,0,26,34,1,0,40
+A Fake phiX Sample,26,36,AA,0,26,35,2,0,40
+A Fake phiX Sample,26,36,AG,0,26,35,1,0,40
+A Fake phiX Sample,26,36,AT,0,26,35,1,0,40
+A Fake phiX Sample,26,36,CT,0,26,35,2,0,40
+A Fake phiX Sample,26,36,GA,0,26,35,1,0,40
+A Fake phiX Sample,26,36,TA,0,26,35,2,0,40
+A Fake phiX Sample,26,36,TG,0,26,35,1,0,40
+EOF
Binary file test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam has changed
Binary file test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains	Mon Apr 14 08:48:25 2014 -0400
@@ -0,0 +1,16 @@
+GenomeAnalysisEngine - Strictness is SILENT
+TableRecalibrationWalker - Reading in the data from input csv file...
+TableRecalibrationWalker - ...done!
+TableRecalibrationWalker - The covariates being used here:
+TableRecalibrationWalker - 	ReadGroupCovariate
+TableRecalibrationWalker - 	QualityScoreCovariate
+TableRecalibrationWalker - 	CycleCovariate
+TableRecalibrationWalker - 	DinucCovariate
+TableRecalibrationWalker - 	HomopolymerCovariate
+TableRecalibrationWalker - 	MinimumNQSCovariate
+TableRecalibrationWalker - 	PositionCovariate
+TableRecalibrationWalker - Generating tables of empirical qualities for use in sequential calculation...
+TableRecalibrationWalker - ...done!
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta	Mon Apr 14 08:48:25 2014 -0400
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
--- a/tool-data/gatk_annotations.txt.sample	Tue Apr 01 10:49:41 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#unique_id	name	gatk_value	tools_valid_for
-AlleleBalance	AlleleBalance	AlleleBalance	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-AlleleBalanceBySample	AlleleBalanceBySample	AlleleBalanceBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-BaseCounts	BaseCounts	BaseCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ChromosomeCounts	ChromosomeCounts	ChromosomeCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-DepthOfCoverage	DepthOfCoverage	DepthOfCoverage	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-DepthPerAlleleBySample	DepthPerAlleleBySample	DepthPerAlleleBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-FisherStrand	FisherStrand	FisherStrand	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-GCContent	GCContent	GCContent	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HaplotypeScore	HaplotypeScore	HaplotypeScore	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HardyWeinberg	HardyWeinberg	HardyWeinberg	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HomopolymerRun	HomopolymerRun	HomopolymerRun	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-InbreedingCoeff	InbreedingCoeff	InbreedingCoeff	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-IndelType	IndelType	IndelType	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-LowMQ	LowMQ	LowMQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZero	MappingQualityZero	MappingQualityZero	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZeroBySample	MappingQualityZeroBySample	MappingQualityZeroBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZeroFraction	MappingQualityZeroFraction	MappingQualityZeroFraction	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-NBaseCount	NBaseCount	NBaseCount	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-QualByDepth	QualByDepth	QualByDepth	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-RMSMappingQuality	RMSMappingQuality	RMSMappingQuality	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ReadPosRankSumTest	ReadPosRankSumTest	ReadPosRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-SampleList	SampleList	SampleList	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-SnpEff	SnpEff	SnpEff	VariantAnnotator,VariantRecalibrator
-SpanningDeletions	SpanningDeletions	SpanningDeletions	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-TechnologyComposition	TechnologyComposition	TechnologyComposition	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
--- a/tool_data_table_conf.xml.sample	Tue Apr 01 10:49:41 2014 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Apr 14 08:48:25 2014 -0400
@@ -5,9 +5,4 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gatk_sorted_picard_index.loc" />
     </table>
-    <!-- Available of GATK references -->
-    <table name="gatk_annotations" comment_char="#">
-        <columns>value, name, gatk_value, tools_valid_for</columns>
-        <file path="tool-data/gatk_annotations.txt" />
-    </table>
 </tables>
--- a/tool_dependencies.xml	Tue Apr 01 10:49:41 2014 -0400
+++ b/tool_dependencies.xml	Mon Apr 14 08:48:25 2014 -0400
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="gatk" version="1.4">
-      <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="gatk" version="1.4">
+        <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" toolshed="http://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" />
     </package>
 </tool_dependency>
--- a/variant_recalibrator.xml	Tue Apr 01 10:49:41 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,431 +0,0 @@
-<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.4">
-  <description></description>
-  <requirements>
-      <requirement type="package" version="1.4">gatk</requirement>
-  </requirements>
-  <macros>
-    <import>gatk_macros.xml</import>
-  </macros>
-  <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #for $var_count, $variant in enumerate( $reference_source.variants ):
-      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
-   #end for
-   -p 'java 
-    -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
-    -T "VariantRecalibrator"
-    --num_threads \${GALAXY_SLOTS:-4}
-    -et "NO_ET" ##ET no phone home
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
-    #if $reference_source.reference_source_selector != "history":
-        -R "${reference_source.ref_file.fields.path}"
-    #end if
-    --recal_file "${output_recal}"
-    --tranches_file "${output_tranches}"
-    --rscript_file "${output_rscript}"
-   '
-    
-    #set $rod_binding_names = dict()
-    #for $rod_binding in $rod_bind:
-        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-        #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
-            #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
-        #else 
-            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
-        #end if
-        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
-            -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #else:
-            -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #end if
-    #end for
-    
-    #include source=$standard_gatk_options#
-    
-    ##start analysis specific options
-    -p '
-    #if str( $annotations ) != "None":
-        #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
-            --use_annotation "${annotation}"
-        #end for
-    #end if
-    #for $additional_annotation in $additional_annotations:
-        --use_annotation "${additional_annotation.additional_annotation_name}"
-    #end for
-    --mode "${mode}"
-    '
-    
-    #if $analysis_param_type.analysis_param_type_selector == "advanced":
-        -p '
-        --maxGaussians "${analysis_param_type.max_gaussians}"
-        --maxIterations "${analysis_param_type.max_iterations}"
-        --numKMeans "${analysis_param_type.num_k_means}"
-        --stdThreshold "${analysis_param_type.std_threshold}"
-        --qualThreshold "${analysis_param_type.qual_threshold}"
-        --shrinkage "${analysis_param_type.shrinkage}"
-        --dirichlet "${analysis_param_type.dirichlet}"
-        --priorCounts "${analysis_param_type.prior_counts}"
-        #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent':
-            --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}"
-        #else:
-            --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}"
-        #end if
-        --target_titv "${analysis_param_type.target_titv}"
-        #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
-            --TStranche "${tranche}"
-        #end for
-        #for $ignore_filter in $analysis_param_type.ignore_filters:
-            #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
-            #if $ignore_filter_name == "custom":
-              #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
-            #end if
-            --ignore_filter "${ignore_filter_name}"
-        #end for
-        --ts_filter_level "${analysis_param_type.ts_filter_level}"
-        '
-    #end if
-    
-    
-    &amp;&amp;
-    mv "${output_rscript}.pdf" "${output_tranches_pdf}"
-    
-  </command>
-  <inputs>
-    <conditional name="reference_source">
-      <expand macro="reference_source_selector_param" />
-      <when value="cached">
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
-        </repeat>
-        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
-          <options from_data_table="gatk_picard_indexes">
-          <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
-          </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"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
-        </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
-      </when>
-    </conditional>
-    
-    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;">
-        <conditional name="rod_bind_type">
-          <param name="rod_bind_type_selector" type="select" label="Binding Type">
-            <option value="dbsnp" selected="True">dbSNP</option>
-            <option value="variant">Variants</option>
-            <option value="snps">SNPs</option>
-            <option value="indels">INDELs</option>
-            <option value="hapmap">HapMap</option>
-            <option value="omni">OMNI</option>
-            <option value="mask">Mask</option>
-            <option value="custom">Custom</option>
-            <option value="comp">Comp</option>
-          </param>
-          <when value="variant">
-              <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="comp">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="mask">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>          
-          <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="snps">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="hapmap">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="omni">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="indels">
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-          <when value="custom">
-              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <conditional name="rod_training_type">
-                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
-                      <option value="is_training_truth_known">Set training/truth/known sites</option>
-                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
-                  </param>
-                  <when value="not_training_truth_known">
-                      <!-- do nothing here -->
-                  </when>
-                  <when value="is_training_truth_known">
-                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
-                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
-                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
-                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
-                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
-                  </when>
-              </conditional>
-          </when>
-        </conditional>
-    </repeat>
-    
-    <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
-      <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
-      <options from_data_table="gatk_annotations">
-        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-        <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
-      </options>
-    </param>
-    
-    <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
-      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
-    </repeat>
-    
-    <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
-        <option value="SNP" selected="True">SNP</option>
-        <option value="INDEL">INDEL</option>
-        <option value="BOTH">BOTH</option>
-    </param>
-    
-    <expand macro="gatk_param_type_conditional" />
-    
-    <expand macro="analysis_type_conditional">
-        <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
-        <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
-        <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
-        <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0" help="-std,--stdThreshold &amp;lt;stdThreshold&amp;gt;"/>
-        <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold &amp;lt;qualThreshold&amp;gt;"/>
-        <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &amp;lt;shrinkage&amp;gt;"/>
-        <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &amp;lt;dirichlet&amp;gt;"/>
-        <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &amp;lt;priorCounts&amp;gt;"/>
-        <conditional name="bad_variant_selector">
-          <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
-            <option value="percent" selected="True">Percent</option>
-            <option value="min_num">Number</option>
-          </param>
-          <when value="percent">
-            <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants &amp;lt;percentBadVariants&amp;gt;"/>
-          </when>
-          <when value="min_num">
-            <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants &amp;lt;minNumBadVariants&amp;gt;"/>
-          </when>
-        </conditional>
-        <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv &amp;lt;target_titv&amp;gt;"/>
-        <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche &amp;lt;TStranche&amp;gt;"/>
-        <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
-          <conditional name="ignore_filter_type">
-            <param name="ignore_filter_type_selector" type="select" label="Filter Type">
-              <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
-              <option value="LowQual" >LowQual</option>
-              <option value="custom" selected="True">Other</option>
-            </param>
-            <when value="custom">
-              <param name="filter_name" type="text" value="" label="Filter name"/>
-            </when>
-            <when value="HARD_TO_VALIDATE" />
-            <when value="LowQual" />
-          </conditional>
-        </repeat>
-        <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
-    <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
-    <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
-    <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
-    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
-  </outputs>
-  <tests>
-      <!-- ADD TESTS -->
-  </tests>
-  <help>
-**What it does**
-
-Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
-
-For more information on using the VariantRecalibrator module, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration&gt;`_.
-
-To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
-
-If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
-
-------
-
-**Inputs**
-
-GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
-
-
-**Outputs**
-
-The output is in VCF format.
-
-
-Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
-
--------
-
-**Settings**::
-
-
- tranches_file         The output tranches file used by ApplyRecalibration
- use_annotation        The names of the annotations which should used for calculations
- mode                  Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously. (SNP|INDEL|BOTH)
- maxGaussians          The maximum number of Gaussians to try during variational Bayes algorithm
- maxIterations         The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
- numKMeans             The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
- stdThreshold          If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.
- qualThreshold         If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.
- shrinkage             The shrinkage parameter in variational Bayes algorithm.
- dirichlet             The dirichlet parameter in variational Bayes algorithm.
- priorCounts           The number of prior counts to use in variational Bayes algorithm.
- percentBadVariants    What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.
- minNumBadVariants     The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary.
- recal_file            The output recal file used by ApplyRecalibration
- target_titv           The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!
- TStranche             The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)
- ignore_filter         If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
- path_to_Rscript       The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript
- rscript_file          The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
- path_to_resources     Path to resources folder holding the Sting R scripts.
- ts_filter_level       The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots
-
-@CITATION_SECTION@
-  </help>
-</tool>