annotate hicInterIntraTAD.xml @ 2:32173084d53f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03

<tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>computes the ratio of inter TAD-scores vs. intra TADs</description>
    <macros>
        <token name="@BINARY@">hicInterIntraTAD</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&

       @BINARY@
            --matrix 'matrix.$matrix_h5_cooler.ext'
            --tadDomains '$tadDomains'

            #if $fontSize:
                --fontSize $fontSize
            #end if

            #if $dpi:
                --dpi $dpi
            #end if

            --outFileName output_interintra.txt
            --outFileNameRatioPlot plot.$image_file_format
            --threads @THREADS@

            && mv plot.$image_file_format plot
            
    ]]>    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param name="tadDomains" type="data" format="bed" label="Bed file with TAD domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />

        <expand macro="dpi" />
        <param name="fontSize" type="integer" min="5" optional="True" label="Font size" help="Font size for the plot"/>
        
        <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_txt' from_work_dir='output_interintra.txt' format='txt' label='Intra Inter TAD ratios'/>

       <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>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="hicInterIntraTAD/matrix.cool" />
            <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" ftype="bed" />
            
            <output name="output_txt" file="hicInterIntraTAD/output.txt" ftype="txt" />
            
            <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" compare="sim_size" delta="10000"/>
            
        </test>
      
    </tests>
    <help><![CDATA[

Calculate the ratio of inter-TAD contacts vs intra-TADs
=======================================================

Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs. 
This tool supports to compute the ratio of contacts of a TAD (intra-TAD) with the contacts outside of it (inter-TAD).

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>