<tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>plots the relation of short vs long range contacts</description>
    <macros>
        <token name="@BINARY@">hicPlotSVL</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            #set identifier = @ESCAPE_IDENTIFIER_M@
            ln -s '$m' '${counter}_$identifier' &&
        #end for
        #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
       
        @BINARY@
            --matrices $m
            #if $distance:
                --distance $distance
            #end if

            @CHROMOSOME_LIST@

            #if $colorList:
                #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
                --colorList $colorList_new
            #end if

            #if $dpi:
                --dpi $dpi
            #end if 
            --plotFileName plot.$image_file_format
            --outFileName p_values.txt
            --outFileNameData ratios.txt 
            --threads @THREADS@

            && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_macro'/>
        <param argument="--distance" optional='true'  type="integer" label="Short range distance"
            help="Distance which should be considered as short range. Default 2MB." value='2000000'/>
        <expand macro="chromosome_list" />
        <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
            <option value="pdf">pdf</option>
        </param>
    </inputs>
    <outputs> 
        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
                <when input="image_file_format" value="pdf" format="pdf" />
            </change_format>
        </data>
        <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl'/>
        <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl'/>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
            <param name="distance" value="2000000"/>
            <param name="dpi" value="10"/>
            <param name="color" value="y m c"/>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chr2L"/>
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chr3L"/>
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chr4"/>
            </repeat>

            <param name="image_file_format" value="png" />

            <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/>
            <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/>
            <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
       
        </test>
    </tests>
    <help><![CDATA[

Short vs long range contacts
============================

Computes the ratio of short vs. long range contacts on the given matrices and makes, if two or more matrices are present a differential test between the matrices.

For more information about HiCExplorer please consider our documentation on readthedocs.io_.

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html

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