<tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@">
    <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    
    <command detect_errors="exit_code"><![CDATA[
        dr-disco
            classify
            
                ${only_valid}
                
                #if $blacklist_regions:
                    --blacklist-regions '${blacklist_regions}'
                #end if

                #if $blacklist_junctions:
                    --blacklist-junctions '${blacklist_junctions}'
                #end if
                
                --min-chim-overhang '${min_chim_overhang}'
                
                '${dr_disco_detect_output}'
                '${dr_disco_classify_output}'
    ]]></command>

    <inputs>
        <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" />
        <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" />
        
        <param name="blacklist_regions"   argument="--blacklist-regions"   type="data" format="bed"     optional="True" label="Blacklist Regions"   help="List of regions known to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />
        <param name="blacklist_junctions" argument="--blacklist-junctions" type="data" format="tabular" optional="True" label="Blacklist Junctions" help="List of junctions know to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />

        <param name="min_chim_overhang" type="integer" min="-1" value="50" label="Minimum alignment length on each side of the junction." help="May need to be set to smaller values for read lengths smaller than 75bp." argument="--min-chim-overhang" />
    </inputs>
    
    <outputs>
        <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" />
    </outputs>
    
    <tests>
        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" value="" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" />
        </test>

        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" value="--only-valid" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" />
        </test>

        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" />
        </test>

        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-04.out.dbed" />
        </test>

        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-05.out.dbed" ftype="tabular" />
        </test>
        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" />
        </test>
        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
            <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-07.out.dbed" ftype="tabular" />
        </test>
        <test>
            <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
            <param name="only_valid" />
            <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
            <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />

            <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" />
        </test>

    </tests>
    
    <help><![CDATA[

**What it does**

It filters fusion events that are likely to be true or false based on a variety of parameters provided in the input table.

**Attributions**

This work is part of Youri Hoogstrate's PhD thesis.

    ]]></help>
    
     <expand macro="citations"/>
</tool>