<tool id="cnvkit_fix" name="CNVkit Fix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Adjust raw coverage data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_target_file' ./tumor.targetcoverage.cnn &&
        #if $input_antitarget_file
            ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
        #end if
        #if $input_reference_coverage_file
            ln -s '$input_reference_coverage_file' ./ref-tas.cnn &&
        #end if
        cnvkit.py fix
            ./tumor.targetcoverage.cnn
            #if $input_antitarget_file
                ./tumor.antitargetcoverage.cnn
            #end if  
            #if $input_reference_coverage_file
                ./ref-tas.cnn 
            #end if  
            --output sample.cnr
            $cluster
            #if $sample_id
                --sample-id '$sample_id'
            #end if
            $no_gc
            $no_edge
            $no_rmask
    ]]></command>
    <inputs>
        <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" />
        <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Sample Antitarget coverage cnn file" help="" />
        <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
        <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
        <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
        <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
        <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
        <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
    </inputs>
    <outputs>
        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
            <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" />
            <param name="input_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" />
            <param name="no_edge" value="1" />
            <output name="out_sample_cnr">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output> 
        </test>
    </tests>
    <help><![CDATA[
        Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases
        in regional coverage and GC content, according to the given reference.
        
        The reference .cnn file output contains those columns
        chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
        of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
        depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
    ]]></help>
    <expand macro="citations" />
</tool>