<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.1">
  <description>- perform local realignment</description>
<command interpreter="python">gatk_wrapper.py
   --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}"
    ##-log "${output_log}"
    ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
    -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R"         
    #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}"
         ${analysis_param_type.do_indel_quality}
    #end if
   '
  </command>
  <inputs>
    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" />
    <conditional name="analysis_param_type">
      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number."/>
        <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups."/>
        <param name="max_quality_score" type="integer" value="50" label="Max quality score"/>
        <param name="max_histogram_value" type="integer" value="0" label="Max quality score"/>
        <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Max quality score"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="html" name="output_html" label="${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.


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Please cite the website "http://addlink.here" as well as:

Add citation here 2011.

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**Input formats**

GenomeAnalysisTK: AnalyzeCovariates accepts an recal CSV file.

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**Outputs**

The output is in and HTML file with links to PDF graphs and a data files, see http://addlink.here for more details.

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**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

  </help>
</tool>