annotate hicCompartmentalization.xml @ 1:c6f32406aa3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"

<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
    <macros>
        <token name="@BINARY@">hicCompartmentalization</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' '${counter}_matrix.$m.ext' &&
        #end for
        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
       
        @BINARY@

            --obsexp_matrices $m

            --pca '$pca'
            --quantile $quantile

            #if $set_offset_value:
                #set $offset_array = $set_offset_value.split(' ')
                #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
                --offset $offset
            #end if
            --outliers $outliers
            --outputFileName plot.$image_file_format

        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_multiple_macro" />
        <param name='pca'  type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with 
                                no header. In case of several matrices with 
                                 different conditions, ie. control
                                treatment, the PCA of control can be 
                                used. Note that only one PCA can be provided.'/>
        <param name='quantile'  type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/>
        <param name='outliers'  type="float"  label="Outliers" help='The number of outliers to be removed.' value="0.0"/>
        <param name="set_offset_value" type="text" value="" label="Offset values" 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 format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
            <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_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'>
            <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
            <param name="quantile" value='30'/>
            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
            <param name="outliers" value='1.0'/>
            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

Comparmentalization
===================

**hicCompartmentalization** rearranges the average interaction frequencies using the first PC values to represent the global compartmentalization signal.
To our knowledge this has been first introduced and implemented by Wibke Schwarzer et al. 2017 (Nature. 2017 Nov 2; 551(7678): 51–56)


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>