<tool id="hicup_truncater" name="Hicup Truncater" version="0.1.0">
    <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <expand macro="stdio" />
    <command><![CDATA[
        hicup_truncater --re1 '$re1' $advanced_options.nofill 
        #if $advanced_options.sequences:
            --sequences '$advanced_options.sequences'
        #end if
        '$input_first_sequence' '$input_second_sequence'

        && mv hicup_truncater_summary* hicup_truncater_summary.txt
        && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
      
        && mv \$trunc_result_1.trunc.fastq dataset1.trunc.fastq
        && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
        && mv \$trunc_result_2.trunc.fastq dataset2.trunc.fastq
        && mv \$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg
        && mv \$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg
        
    ]]></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>
       <expand macro="truncater_output" />

    </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" lines_diff="8" />
            <output name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/>
            <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>