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1 <tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.5">
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2 <description>- draw plots</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 </requirements>
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6 <macros>
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7 <import>gatk_macros.xml</import>
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8 </macros>
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9 <command interpreter="python">gatk_wrapper.py
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10 --max_jvm_heap_fraction "1"
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11 --stdout "${output_log}"
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12 --html_report_from_directory "${output_html}" "${output_html.files_path}"
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13 -p 'java
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14 -jar "${JAVA_JAR_PATH}/AnalyzeCovariates.jar"
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15 -recalFile "${input_recal}"
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16 -outputDir "${output_html.files_path}"
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17 ##--num_threads 4 ##hard coded, for now
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18 ##-log "${output_log}"
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19 ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
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20 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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21 --ignoreQ "${analysis_param_type.ignore_q}"
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22 --numRG "${analysis_param_type.num_read_groups}"
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23 --max_quality_score "${analysis_param_type.max_quality_score}"
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24 --max_histogram_value "${analysis_param_type.max_histogram_value}"
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25 ${analysis_param_type.do_indel_quality}
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26 #end if
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27 '
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28 </command>
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29 <inputs>
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30 <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" />
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31 <conditional name="analysis_param_type">
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32 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced options">
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33 <option value="basic" selected="True">Basic</option>
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34 <option value="advanced">Advanced</option>
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35 </param>
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36 <when value="basic">
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37 <!-- Do nothing here -->
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38 </when>
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39 <when value="advanced">
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40 <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number." help="-ignoreQ,--ignoreQ &lt;ignoreQ&gt; "/>
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41 <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups." help="-numRG,--numRG &lt;numRG&gt;"/>
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42 <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &lt;max_quality_score&gt;"/>
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43 <param name="max_histogram_value" type="integer" value="0" label="Max histogram value" help="-maxHist,--max_histogram_value &lt;max_histogram_value&gt;"/>
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44 <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality" help="--do_indel_quality"/>
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45 </when>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)" />
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50 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
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55 <param name="analysis_param_type_selector" value="basic" />
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56 <output name="output_html" file="gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html" />
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57 <output name="output_log" file="gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.log.contains" compare="contains" />
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58 </test>
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59 </tests>
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60 <help>
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61 **What it does**
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62
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63 Create collapsed versions of the recal csv file and call R scripts to plot residual error versus the various covariates.
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64
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65 For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration>`_.
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66
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67 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
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68
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69 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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70
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71 ------
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72
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73 **Inputs**
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74
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75 GenomeAnalysisTK: AnalyzeCovariates accepts an recal CSV file.
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76
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77
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78 **Outputs**
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79
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80 The output is in CSV and HTML files with links to PDF graphs and a data files.
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81
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82
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83 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
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84
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85 -------
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86
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87 **Settings**::
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88
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89 recal_file The input recal csv file to analyze
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90 output_dir The directory in which to output all the plots and intermediate data files
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91 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
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92 path_to_resources Path to resources folder holding the Sting R scripts.
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93 ignoreQ Ignore bases with reported quality less than this number.
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94 numRG Only process N read groups. Default value: -1 (process all read groups)
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95 max_quality_score The integer value at which to cap the quality scores, default is 50
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96 max_histogram_value If supplied, this value will be the max value of the histogram plots
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97 do_indel_quality If supplied, this value will be the max value of the histogram plots
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98
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99 @CITATION_SECTION@
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100 </help>
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101 </tool>
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