<?xml version="1.0"?>
<tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>tanscript selector for BRAKER</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    tsebra.py 

    #if str( $gtf_file_param ) == "GTF":
        -g '$gtf_input'
    #elif str( $gtf_file_param ) == "KEEP_GTF":
        -k '$gtf_input'
    #end if

    #if $hint_file
        -e '$hint_file'
    #end if
    #if $cfg_file
        -c '$cfg_file'
    #end if

    $ignore_tx_phase
    #if $filter_exon
        --filter_single_exon_genes
    #end if
    #if $score_tab
        --score_tab '$output_tab'
    #end if 

    -o '$output' 
    ]]></command>
    <inputs>
        <param name="gtf_input" type="data" format="gtf" label="GTF input"/>
        <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file">
            <option value="GTF" selected="true">List of gene prediciton files</option>
            <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option>
        </param>
        <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
        <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/>
        <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
        <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
        <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
        <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>    
    </inputs>

    <outputs>
        <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
        <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
            <actions>
                <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" />
            </actions>
            <filter>score_tab</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
            <param name="score_tab" value="false"/>
            <param name="gtf_file_param" value="GTF"/>
            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
        </test>
        
        <test expect_num_outputs="2">
            <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
            <param name="score_tab" value="true"/>
            <param name="gtf_file_param" value="GTF"/>
            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
            <output name="output_tab" ftype="txt">
                <assert_contents>
                    <has_size value="32000" delta="300"/>
                    <has_text text="anno1;g1.t1"/>
                    <has_text text="anno1;g59.t1"/>
                    <has_text text="anno1;g169.t1"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
        tsebra_  TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence 
        in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.


        .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
    ]]></help> 
    <expand macro="citation"></expand>
</tool>