<tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@.0">
    <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <command detect_errors="exit_code"><![CDATA[
        ##Dealing with fastq and fastq.gz
        #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
           ln -s $input_first_sequence dataset1.gz &&
           #set input1='dataset1.gz'
        #else
           ln -s $input_first_sequence dataset1 &&
           #set input1='dataset1'
        #end if
        
        #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
            ln -s $input_second_sequence dataset2.gz &&
            #set input2='dataset2.gz'
        #else
            ln -s $input_second_sequence dataset2 &&
            #set input2='dataset2'
        #end if
        
        hicup_truncater --zip --re1 '$re1' $advanced_options.nofill 
        #if $advanced_options.sequences:
            --sequences '$advanced_options.sequences'
        #end if
        $input1 $input2
    ]]></command>
    <inputs>
        <expand macro="input_files" />
        <expand macro="re1" />
        <section name="advanced_options" title="Advanced options">
            <expand macro="no_fill" />
            <param argument="--sequences" type="text" value="" label="Ligation sequence" help="Instead of specifying a restriction enzyme recognition sequence, specify the ligation sequences directly"/>
        </section>
    </inputs>
    <outputs>
        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" />
        <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" />
        <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" />
        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" />
        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" />
    </outputs>
    <tests>
        <test>
            <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
            <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
            <param name="re1" value="A^AGCTT"/>
            
            <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>
            <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/>
            <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/>
            <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
            <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
        </test>
    </tests>
    <help><![CDATA[

    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/

    To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
    ]]></help>

   <expand macro="citation_hicup" />
</tool>