gatk4_plotdenoisedcopyratios.xml

<tool id="gatk4_plotdenoisedcopyratios" name="GATK4 PlotDenoisedCopyRatios" profile="17.09" version="@WRAPPER_VERSION@0">
  <description>- Creates plots of denoised copy ratios</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="version_cmd"/>
  <command detect_errors="exit_code"><![CDATA[#include source=$bam_index#
#include source=$pre_gatk_ints_chth#
#include source=$pre_gatk_excl_ints_chth#
@CMD_BEGIN@ PlotDenoisedCopyRatios
#if $denoised_copy_ratios:
--denoised-copy-ratios $denoised_copy_ratios
#end if
#if $optional.gcs_max_retries:
--gcs-max-retries $optional.gcs_max_retries
#end if
#if $optional.minimum_contig_length:
--minimum-contig-length $optional.minimum_contig_length
#end if
#if $output_prefix:
--output-prefix $output_prefix
#end if
#if $sequence_dictionary:
--sequence-dictionary $sequence_dictionary
#end if
#if $standardized_copy_ratios:
--standardized-copy-ratios $standardized_copy_ratios
#end if
#include source=$ref_opts_opt#
#include source=$vcf_output_opts#
#include source=$gatk_bam_input#
#include source=$gatk_ints_chth#
#include source=$gatk_excl_ints_chth#]]></command>
  <inputs>
    <expand macro="ref_sel"/>
    <expand macro="gatk_req_params"/>
    <expand macro="picard_vcf_params"/>
    <expand macro="gatk_ints"/>
    <expand macro="gatk_excl_ints"/>
    <param name="denoised_copy_ratios" argument="--denoised-copy-ratios" type="data" optional="false" format="" label="Denoised Copy Ratios" help="Input file containing denoised copy ratios (output of DenoiseReadCounts)."/>
    <param name="output_prefix" argument="--output-prefix" type="text" optional="false" value="" label="Output Prefix" help="Prefix for output filenames."/>
    <param name="sequence_dictionary" argument="--sequence-dictionary" type="data" optional="false" format="" label="Sequence Dictionary" help="File containing a sequence dictionary, which specifies the contigs to be plotted and their relative lengths. The sequence dictionary must be a subset of those contained in other input files. Contigs will be plotted in the order given. Contig names should not include the string &amp;quot;CONTIG_DELIMITER&amp;quot;. The tool only considers contigs in the given dictionary for plotting, and data for contigs absent in the dictionary generate only a warning. In other words, you may modify a reference dictionary for use with this tool to include only contigs for which plotting is desired, and sort the contigs to the order in which the plots should display the contigs."/>
    <param name="standardized_copy_ratios" argument="--standardized-copy-ratios" type="data" optional="false" format="" label="Standardized Copy Ratios" help="Input file containing standardized copy ratios (output of DenoiseReadCounts)."/>
    <section expanded="False" name="optional" title="Optional Parameters">
      <param name="gcs_max_retries" argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
      <param name="minimum_contig_length" argument="--minimum-contig-length" type="integer" optional="true" value="1000000" label="Minimum Contig Length" help="Threshold length (in bp) for contigs to be plotted. Contigs with lengths less than this threshold will not be plotted. This can be used to filter out mitochondrial contigs, unlocalized contigs, etc."/>
    </section>
    <section expanded="False" name="common" title="Common Parameters">
      <param name="gatk_config_file" argument="--gatk-config-file" type="data" optional="true" format="txt" label="Gatk Config File" help="A configuration file to use with the GATK."/>
      <param name="use_jdk_deflater" argument="--use-jdk-deflater" type="boolean" truevalue="--use-jdk-deflater" falsevalue="" optional="true" checked="false" label="Use Jdk Deflater" help="Whether to use the JdkDeflater (as opposed to IntelDeflater)"/>
      <param name="use_jdk_inflater" argument="--use-jdk-inflater" type="boolean" truevalue="--use-jdk-inflater" falsevalue="" optional="true" checked="false" label="Use Jdk Inflater" help="Whether to use the JdkInflater (as opposed to IntelInflater)"/>
      <param name="verbosity" argument="--verbosity" type="select" optional="true" label="Verbosity" help="Control verbosity of logging.">
        <option selected="false" value="ERROR">ERROR</option>
        <option selected="false" value="WARNING">WARNING</option>
        <option selected="true" value="INFO">INFO</option>
        <option selected="false" value="DEBUG">DEBUG</option>
      </param>
    </section>
  </inputs>
  <outputs>
    <expand macro="picard_vcf_output_params"/>
  </outputs>
  <tests/>
  <help><![CDATA[Creates plots of denoised copy ratios. The tool also generates various
denoising metrics.

Inputs
~~~~~~

-  Standardized-copy-ratios from DenoiseReadCounts.
-  Denoised-copy-ratios from DenoiseReadCounts.
-  Sequence-dictionary file. This determines the order and
   representation of contigs in the plot.
-  Output prefix. This is used as the basename for output files.
-  Output directory. This must be a pre-existing directory.

Outputs
~~~~~~~

-  Denoised-plot files. Two versions of a plot showing both the
   standardized and denoised copy ratios are output; the first covers
   the entire range of the copy ratios, while the second is limited to
   copy ratios within [0, 4].
-  Median-absolute-deviation files. These files contain the median
   absolute deviation (MAD) for both the standardized
   (.standardizedMAD.txt) and denoised (.denoisedMAD.txt) copy ratios,
   the change between the two (.deltaMAD.txt), and the change between
   the two scaled by the standardized MAD (.deltaScaledMAD.txt).

Usage example
~~~~~~~~~~~~~

::

        gatk PlotDenoisedCopyRatios \
             --standardized-copy-ratios tumor.standardizedCR.tsv \
             --denoised-copy-ratios tumor.denoisedCR.tsv \
             --sequence-dictionary contigs_to_plot.dict \
             --output-prefix tumor \
             -O output_dir
    
]]></help>
  <citations>
    <expand macro="citations"/>
  </citations>
</tool>