/tools/gatk/variant_filtration.xml

<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.5">
  <description>on VCF files</description>
  <requirements>
      <requirement type="package" version="1.4">gatk</requirement>
  </requirements>
  <macros>
    <import>gatk_macros.xml</import>
  </macros>
  <command interpreter="python">gatk_wrapper.py
   #from binascii import hexlify
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
   -p 'java 
    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
    -T "VariantFiltration"
    ##--num_threads 4 ##hard coded, for now
    -et "NO_ET" ##ET no phone home
    -o "${output_vcf}"
    ##-log "${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
    '
    #for $variant_filter in $variant_filters:
        #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name )  )
        -o '${ hexlify( $variant_filter ) }'
    #end for
    
    #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask':
        -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}"
        -p '
        --maskExtension "${mask_rod_bind_type.mask_extension}"
        --maskName "${mask_rod_bind_type.mask_rod_name}"
        '
    #end if
    
    #include source=$standard_gatk_options#
    
    ##start analysis specific options
    #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp":
        -p '
        --clusterSize "${cluster_snp_type.cluster_size}"
        --clusterWindowSize "${cluster_snp_type.cluster_window_size}"
        '
    #end if
    -p '${missing_values_in_expressions_should_evaluate_as_failing}'
  </command>
  <inputs>
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
        <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_variant" 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!!!! -->
        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
        <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="variant_filters" title="Variant Filters">
        <param name="filter_expression" value="AB &lt; 0.2 || MQ0 &gt; 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &amp;lt;filterExpression&amp;gt;)">
            <sanitizer>
              <valid initial="string.printable">
               <remove value="&apos;"/>
             </valid>
              <mapping initial="none"/>
            </sanitizer>
        </param>
        <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &amp;lt;filterName&amp;gt;"/>
        <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &amp;lt;genotypeFilterExpression&amp;gt; and -G_filterName,--genotypeFilterName &amp;lt;genotypeFilterName&amp;gt; for filter type" />
    </repeat>
    

    
    <conditional name="mask_rod_bind_type">
      <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
        <option value="set_mask" selected="True">Set maskP</option>
        <option value="exclude_mask">Don't set mask</option>
      </param>
      <when value="exclude_mask">
        <!-- Do nothing here -->
      </when>
      <when value="set_mask">
        <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &amp;lt;mask&amp;gt;" />
        <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &amp;lt;maskName&amp;gt;"/>
        <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &amp;lt;maskExtension&amp;gt;"/>
      </when>
    </conditional>    
    
    
    <expand macro="gatk_param_type_conditional" />
    
    <conditional name="cluster_snp_type">
      <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs">
        <option value="cluster_snp">Cluster SNPs</option>
        <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option>
      </param>
      <when value="do_not_cluster_snp">
        <!-- Do nothing here -->
      </when>
      <when value="cluster_snp">
        <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &amp;lt;clusterSize&amp;gt;"/>
        <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &amp;lt;clusterWindowSize&amp;gt;"/>
      </when>
    </conditional>
    
    <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" />
    
  </inputs>
  <outputs>
    <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
  </outputs>
  <tests>
      <test>
          <param name="reference_source_selector" value="history" />
          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
          <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
          <param name="filter_expression" value="MQ &lt; 37.74 || MQ0 &gt; 50" />
          <param name="filter_name" value="Galaxy_filter" />
          <param name="is_genotype_filter" />
          <param name="mask_rod_bind_type_selector" value="set_mask" />
          <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
          <param name="mask_rod_name" value="." />
          <param name="mask_extension" value="0" />
          <param name="gatk_param_type_selector" value="basic" />
          <param name="cluster_snp_type_selector" value="do_not_cluster_snp" />
          <param name="missing_values_in_expressions_should_evaluate_as_failing" />
          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> 
          <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**

Filters variant calls using a number of user-selectable, parameterizable criteria.

For more information on using the VariantFiltration module, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/VariantFiltrationWalker&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: VariantFiltration accepts a VCF 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**::


 filterExpression                                     One or more expression used with INFO fields to filter (see wiki docs for more info)
 filterName                                           Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
 genotypeFilterExpression                             One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info)
 genotypeFilterName                                   Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
 clusterSize                                          The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3]
 clusterWindowSize                                    The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0]
 maskName                                             The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']
 missingValuesInExpressionsShouldEvaluateAsFailing    When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?

@CITATION_SECTION@
  </help>
</tool>