<?xml version="1.0" encoding="utf-8"?>
<tool id="gatk" name="GATK" version="@VERSION@.d9">
  <description>tool collection Version @VERSION@</description>
  <macros>
    <import>gatk_macros.xml</import>
    <import>realigner_target_creator.xml</import>
    <import>indel_realigner.xml</import>
    <import>base_recalibrator.xml</import>
    <import>analyze_covariates.xml</import>
    <import>print_reads.xml</import>
    <import>haplotype_caller.xml</import>
    <import>genotype_gvcfs.xml</import>
    <import>combine_gvcfs.xml</import>
    <import>combine_variants.xml</import>
  </macros>
  <expand macro="requirements"/>
  <stdio>
    <regex match="^INFO" level="log"/>
    <regex match="^WARN" level="warning"/>
    <regex match="Using .* implementation of PairHMM" level="warning"/>
    <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal"/>
    <regex match="^##### ERROR" level="fatal"/>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <command><![CDATA[
        ############################
        ## import analysis specific preprocessings by using cheetahs internal searchList
        ## if not defined, ignore
        ############################
        #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2]
            #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"]
            #include source=$analysisPreprocessing
        #end if
        
        ############################
        ## GATK tool unspecific options
        ############################
        @GATK_EXEC@
        
        --analysis_type ${analysis_type.analysis_type_selector}
        --reference_sequence    ${ref_file.fields.path}

        --log_to_file           ${output_log}

        #if $cond_intervals.cond_intervals_enabled
            #for $interval in $cond_intervals.intervals:
                --intervals ${interval.L}
            #end for
        #end if

        #if $cond_BQSR.cond_BQSR_enabled
          --BQSR $cond_BQSR.BQSR
        #end if

        ############################
        ## import analysis specific options by using cheetahs internal searchList
        ## if not defined throw raw python error until better idea
        ############################
        #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2]
            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
            #include source=$analysisOptions
        #else
            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
        #end if
        
        ############################
        ## only put ERROR or FATAL log messages into stderr
        ## but keep full log for printing into log file
        ############################
        2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2
]]></command>
  <inputs>
    <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &amp;lt;reference_sequence&amp;gt;">
      <options from_data_table="picard_indexes"/>
      <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
    </param>
    <conditional name="cond_intervals">
      <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?"/>
      <when value="true">
        <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &amp;lt;intervals&amp;gt;">
          <param name="L" type="text" value=""/>
        </repeat>
      </when>
      <when value="false"/>
    </conditional>
    <conditional name="cond_BQSR">
      <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?"/>
      <when value="true">
        <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &amp;lt;BQSR&amp;gt; intended primarily for use with BaseRecalibrator and PrintReads"/>
      </when>
      <when value="false"/>
    </conditional>
    <conditional name="cond_threads">
      <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?"/>
      <when value="true">
        <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool"/>
        <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool"/>
        <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread"/>
      </when>
      <when value="false"/>
    </conditional>
    <conditional name="analysis_type">
      <param name="analysis_type_selector" type="select" label="Analysis Type">
        <option value="RealignerTargetCreator">RealignerTargetCreator</option>
        <option value="IndelRealigner">IndelRealigner</option>
        <option value="BaseRecalibrator">BaseRecalibrator</option>
        <option value="AnalyzeCovariates">AnalyzeCovariates</option>
        <option value="PrintReads">PrintReads</option>
        <option value="HaplotypeCaller">HaplotypeCaller</option>
        <option value="GenotypeGVCFs">GenotypeGVCFs</option>
        <option value="CombineGVCFs">CombineGVCFs</option>
        <option value="CombineVariants">CombineVariants</option>
      </param>
      <when value="RealignerTargetCreator">
        <expand macro="RealignerTargetCreatorParameters" tag="rtc"/>
      </when>
      <when value="IndelRealigner">
        <expand macro="IndelRealignerParameters" tag="ir"/>
      </when>
      <when value="BaseRecalibrator">
        <expand macro="BaseRecalibratorParameters" tag="br"/>
      </when>
      <when value="AnalyzeCovariates">
        <expand macro="AnalyzeCovariatesParameters" tag="ac"/>
      </when>
      <when value="PrintReads">
        <expand macro="PrintReadsParameters" tag="pr"/>
      </when>
      <when value="HaplotypeCaller">
        <expand macro="HaplotypeCallerParameters" tag="hc"/>
      </when>
      <when value="GenotypeGVCFs">
        <expand macro="GenotypeGVCFsParameters" tag="gg"/>
      </when>
      <when value="CombineGVCFs">
        <expand macro="CombineGVCFsParameters" tag="cg"/>
      </when>
      <when value="CombineVariants">
        <expand macro="CombineVariantsParameters" tag="cv"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <expand macro="RealignerTargetCreatorOutput" tag="rtc">
      <filter>analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'</filter>
    </expand>
    <expand macro="IndelRealignerOutput" tag="ir">
      <filter>analysis_type['analysis_type_selector'] == 'IndelRealigner'</filter>
    </expand>
    <expand macro="BaseRecalibratorOutput" tag="br">
      <filter>analysis_type['analysis_type_selector'] == 'BaseRecalibrator'</filter>
    </expand>
    <expand macro="AnalyzeCovariatesOutput" tag="ac">
      <filter>analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'</filter>
    </expand>
    <expand macro="PrintReadsOutput" tag="pr">
      <filter>analysis_type['analysis_type_selector'] == 'PrintReads'</filter>
    </expand>
    <expand macro="HaplotypeCallerOutput" tag="hc">
      <filter>analysis_type['analysis_type_selector'] == 'HaplotypeCaller'</filter>
    </expand>
    <expand macro="GenotypeGVCFsOutput" tag="gg">
      <filter>analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'</filter>
    </expand>
    <expand macro="CombineGVCFsOutput" tag="cg">
      <filter>analysis_type['analysis_type_selector'] == 'CombineGVCFs'</filter>
    </expand>
    <expand macro="CombineVariantsOutput" tag="cv">
      <filter>analysis_type['analysis_type_selector'] == 'CombineVariants'</filter>
    </expand>
    <data format="txt" name="output_log" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (log)"/>
  </outputs>
  <expand macro="macro_tests"/>
  <citations>
    <citation type="doi">10.1101/gr.107524.110</citation>
    <citation type="doi">10.1038/ng.806</citation>
    <citation type="doi">10.1002/0471250953.bi1110s43</citation>
  </citations>
</tool>