<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.5">
  <description>- draw plots</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 "${output_log}"
   --html_report_from_directory "${output_html}" "${output_html.files_path}"
   -p 'java 
    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar"
    -recalFile "${input_recal}"
    -outputDir "${output_html.files_path}"
    ##--num_threads 4 ##hard coded, for now
    ##-log "${output_log}"
    ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough         
    #if $analysis_param_type.analysis_param_type_selector == "advanced":
        --ignoreQ "${analysis_param_type.ignore_q}"
        --numRG "${analysis_param_type.num_read_groups}"
        --max_quality_score "${analysis_param_type.max_quality_score}"
        --max_histogram_value "${analysis_param_type.max_histogram_value}"
         ${analysis_param_type.do_indel_quality}
    #end if
   '
  </command>
  <inputs>
    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
    <conditional name="analysis_param_type">
      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number." help="-ignoreQ,--ignoreQ &amp;lt;ignoreQ&amp;gt; "/>
        <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups." help="-numRG,--numRG &amp;lt;numRG&amp;gt;"/>
        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
        <param name="max_histogram_value" type="integer" value="0" label="Max histogram value" help="-maxHist,--max_histogram_value &amp;lt;max_histogram_value&amp;gt;"/>
        <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality" help="--do_indel_quality"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)" />
    <data format="txt" name="output_log" label="${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="analysis_param_type_selector" value="basic" />
          <output name="output_html" file="gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html" />
          <output name="output_log" file="gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.log.contains" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**

Create collapsed versions of the recal csv file and call R scripts to plot residual error versus the various covariates.

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: AnalyzeCovariates accepts an recal CSV file.


**Outputs**

The output is in CSV and HTML files with links to PDF graphs and a data files.


Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.

-------

**Settings**::

 recal_file             The input recal csv file to analyze
 output_dir             The directory in which to output all the plots and intermediate data files
 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
 path_to_resources      Path to resources folder holding the Sting R scripts.
 ignoreQ                Ignore bases with reported quality less than this number.
 numRG                  Only process N read groups. Default value: -1 (process all read groups)
 max_quality_score      The integer value at which to cap the quality scores, default is 50
 max_histogram_value    If supplied, this value will be the max value of the histogram plots
 do_indel_quality       If supplied, this value will be the max value of the histogram plots

@CITATION_SECTION@
  </help>
</tool>