<tool id="compareSTR" name="CompareSTR" version="@tool_version@">
    <description>CompareSTR compares different TR callsets generated on the same samples against the same reference
        panel. CompareSTR outputs overall, per-locus, and per-sample concordance information.
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <version_command>compareSTR --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
	@INDEX_VCFS@
    #set $old_names = [$str($required_arguments.vcf1), $str($required_arguments.vcf2)]
    #set $new_names = $get_new_vcf_names($old_names)
    $index_vcfs($old_names, $new_names)

	compareSTR

## end h definition
## vcf1 definition
#if $required_arguments.vcf1:
   --vcf1 $new_names[0]
#end if
## end vcf1 definition
## vcf2 definition
#if $required_arguments.vcf2:
   --vcf2 $new_names[1]
#end if
## end vcf2 definition
## out definition
#if $required_arguments.out:
   --out $required_arguments.out
#end if
## end out definition
## samples definition
#if $filtering_options.samples:
   --samples $filtering_options.samples
#end if
## end samples definition
## region definition
#if $filtering_options.region:
   --region $filtering_options.region
#end if
## end region definition
## stratify_fields definition
#if $metrics_to_stratify_results.stratify_fields:
   --stratify-fields $metrics_to_stratify_results.stratify_fields
#end if
## end stratify_fields definition
## stratify_binsizes definition
#if $metrics_to_stratify_results.stratify_binsizes:
   --stratify-binsizes $metrics_to_stratify_results.stratify_binsizes
#end if
## end stratify_binsizes definition
## stratify_file definition
#if $metrics_to_stratify_results.stratify_file:
   --stratify-file $metrics_to_stratify_results.stratify_file
#end if
## end stratify_file definition
## period definition
#if $metrics_to_stratify_results.period:
   --period
#end if
## end period definition
## bubble_min definition
#if $plotting_options.bubble_min:
   --bubble-min $plotting_options.bubble_min
#end if
## end bubble_min definition
## bubble_max definition
#if $plotting_options.bubble_max:
   --bubble-max $plotting_options.bubble_max
#end if
## end bubble_max definition
## verbose definition
#if $optional_arguments.verbose:
   --verbose
#end if
## end verbose definition
## numrecords definition
#if $optional_arguments.numrecords:
   --numrecords $optional_arguments.numrecords
#end if
## end numrecords definition
## noplot definition
#if $optional_arguments.noplot:
   --noplot
#end if
## end noplot definition
## vcftype1 definition
#if $optional_arguments.vcftype1:
   --vcftype1 $optional_arguments.vcftype1
#end if
## end vcftype1 definition
## vcftype2 definition
#if $optional_arguments.vcftype2:
   --vcftype2 $optional_arguments.vcftype2
#end if
## end vcftype2 definition
## ignore_phasing definition
#if $optional_arguments.ignore_phasing:
   --ignore-phasing
#end if
## end ignore_phasing definition
## version definition
#if $versiondc8f.version:
   --version
#end if
## end version definition
1>$stdout 2>$stderr
]]></command>


    <inputs>
        <section name="required_arguments" title="Required arguments" expanded="false">
            <param argument="--vcf1" type="data" format="vcf_bgzip" optional="false" label="vcf1"
                   help="First VCF file to compare (must be sorted, bgzipped, and indexed)"/>
            <param argument="--vcf2" type="data" format="vcf_bgzip" optional="false" label="vcf2"
                   help="Second VCF file to compare (must be sorted, bgzipped, and indexed)"/>
            <param argument="--out" type="text" optional="false" label="out" help="Prefix to name output files"/>
        </section>
        <section name="filtering_options" title="Filtering options" expanded="false">
            <param argument="--samples" type="text" optional="true" label="samples"
                   help="File containing list of samples to include"/>
            <param argument="--region" type="text" optional="true" label="region"
                   help="Restrict to this region chrom:start-end"/>
        </section>
        <section name="metrics_to_stratify_results" title="Metrics to stratify results" expanded="false">
            <param argument="--stratify-fields" type="text" optional="true" label="stratify_fields"
                   help="Comma-separated list of FORMAT fields to stratify by"/>
            <param argument="--stratify-binsizes" type="text" optional="true" label="stratify_binsizes"
                   help="Comma-separated list of min:max:binsize to stratify each field on. Must be same length as --stratify-fields."/>
            <param argument="--stratify-file" type="integer" optional="true" label="stratify_file"
                   help="Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply stratification to both --vcf1 and --vcf2"/>
            <param argument="--period" type="boolean" optional="true" label="period"
                   help="Report results overall and also stratified by repeat unit length (period)"/>
        </section>
        <section name="plotting_options" title="Plotting options" expanded="false">
            <param argument="--bubble-min" type="integer" optional="true" label="bubble_min"
                   help="Minimum x/y axis value to display on bubble plots"/>
            <param argument="--bubble-max" type="integer" optional="true" label="bubble_max"
                   help="Maximum x/y axis value to display on bubble plots"/>
        </section>
        <section name="optional_arguments" title="Optional arguments" expanded="false">
            <param argument="--verbose" type="boolean" optional="true" label="verbose"
                   help="Print helpful debugging info"/>
            <param argument="--numrecords" type="integer" optional="true" label="numrecords"
                   help="For debugging, only process this many records"/>
            <param argument="--noplot" type="boolean" optional="true" label="noplot"
                   help="Don't output any plots. Only produce text output"/>
            <param argument="--vcftype1" type="select" optional="true" label="vcftype1"
                   help="Genotyper that was used to create this VCF input">
                <expand macro="vcfTypes"/>
            </param>
            <param argument="--vcftype2" type="select" optional="true" label="vcftype2"
                   help="Genotyper that was used to create this VCF input">
                <expand macro="vcfTypes"/>
            </param>
            <param argument="--ignore-phasing" type="boolean" optional="true" label="ignore_phasing"
                   help="Treat all calls as if they are unphased"/>
        </section>
        <section name="versiondc8f" title="Version" expanded="false">
            <param argument="--version" type="boolean" optional="true" label="version"
                   help="show program's version number and exit"/>
        </section>
    </inputs>


    <outputs>
        <data name="stdout" label="STDOUT output" format="txt"/>
        <data name="stderr" label="STDERR output" format="txt"/>

        <collection format="pdf" name="pdfOutput" type="list" label="PDF output">
            <discover_datasets format="pdf" pattern="(?P&lt;designation&gt;.+)\.pdf"/>
        </collection>

        <collection format="tabular" name="tabularOutput" type="list" label="Text file output">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab"/>
        </collection>
    </outputs>


    <tests>
        <test>
            <section name="required_arguments">
                <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
                <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
                <param name="out" value="test_result"/>
            </section>

            <section name="metrics_to_stratify_results">
                <param name="stratify_fields" value="DP,Q"/>
                <param name="stratify_binsizes" value="0:50:5,0:1:0.1"/>
                <param name="stratify_file" value="0"/>
            </section>
            <section name="optional_arguments">
                <param name="verbose" value="true"/>
                <param name="vcftype1" value="hipstr"/>
                <param name="vcftype2" value="hipstr"/>
            </section>

            <output name="stdout" file="stdout.txt"/>
            <output name="stderr" file="stderr.txt"/>

            <output_collection name="pdfOutput" type="list">
                <element name="test_result-bubble-periodALL">
                    <assert_contents>
                        <has_size value="24771" delta="200"/>
                    </assert_contents>
                </element>
                <element name="test_result-locuscompare">
                    <assert_contents>
                        <has_size value="12800" delta="200"/>
                    </assert_contents>
                </element>
                <element name="test_result-samplecompare">
                    <assert_contents>
                        <has_size value="9247" delta="200"/>
                    </assert_contents>
                </element>

            </output_collection>
            <output_collection name="tabularOutput" type="list">
                <element name="test_result-overall" file="test_result-overall.tab"/>
                <element name="test_result-locuscompare" file="test_result-locuscompare.tab"/>
                <element name="test_result-samplecompare" file="test_result-samplecompare.tab"/>
            </output_collection>
        </test>
    </tests>


    <help>usage: pygalgen [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION]
                [--stratify-fields STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES]
                [--stratify-file STRATIFY_FILE] [--period] [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX]
                [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1 VCFTYPE1] [--vcftype2 VCFTYPE2]
                [--ignore-phasing] [--version]

options:
  -h, --help            show this help message and exit

Required arguments:
  --vcf1 VCF1           First VCF file to compare (must be sorted, bgzipped, and indexed)
  --vcf2 VCF2           Second VCF file to compare (must be sorted, bgzipped, and indexed)
  --out OUT             Prefix to name output files

Filtering options:
  --samples SAMPLES     File containing list of samples to include
  --region REGION       Restrict to this region chrom:start-end

Metrics to stratify results:
  --stratify-fields STRATIFY_FIELDS
                        Comma-separated list of FORMAT fields to stratify by
  --stratify-binsizes STRATIFY_BINSIZES
                        Comma-separated list of min:max:binsize to stratify each field on. Must be same length as
                        --stratify-fields.
  --stratify-file STRATIFY_FILE
                        Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply
                        stratification to both --vcf1 and --vcf2
  --period              Report results overall and also stratified by repeat unit length (period)

Plotting options:
  --bubble-min BUBBLE_MIN
                        Minimum x/y axis value to display on bubble plots
  --bubble-max BUBBLE_MAX
                        Maximum x/y axis value to display on bubble plots

Optional arguments:
  --verbose             Print helpful debugging info
  --numrecords NUMRECORDS
                        For debugging, only process this many records
  --noplot              Don't output any plots. Only produce text output
  --vcftype1 VCFTYPE1   Name of genotyper that created the first vcf
  --vcftype2 VCFTYPE2   Name of genotyper that created the second vcf
  --ignore-phasing      Treat all calls as if they are unphased

Version:
  --version             show program's version number and exit
    </help>


    <citations>
        <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
            author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
            year = {2020},
            title = {TRTools},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/gymreklab/trtools},
            }
        </citation>
    </citations>
</tool>