annotate hicPlotViewpoint.xml @ 0:58d146c74d72 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>computes the principal components for A / B compartment analysis</description>
    <macros>
        <token name="@BINARY@">hicPlotViewpoint</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        hicPlotViewpoint --matrix '$matrix_h5_cooler'
        #if $interactionOutFileName:
            $interactionOutFileName interactions.bedgraph
        #end if
        --outFileName plot.$image_file_format
        --region $region
        --referencePoint $referencePoint
        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <expand macro="region" />
        <param name="referencePoint" type="text" label="Reference point"
            help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
   
        <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
                            label="Create bedgraph file with interactions" />
        <param name="image_file_format" type="select" label="Image output format">
            <option value="png">png</option>
            <option value="svg">svg</option>
        </param>

    </inputs>
    <outputs>
       
        <data format="png" name="outFileName" from_work_dir="plot">
            <change_format>
                <when input="image_file_format" value="png" format="png" />
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>
        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'>
            <filter>interactionOutFileName</filter>
        </data>
        
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000' />
            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000-3300000' />
            <param name='interactionOutFileName' value='True' />
            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
            <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
            
        </test>
    </tests>
    <help><![CDATA[
Principal component analysis
============================
`hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.

Input
-----
- the matrix to be analysed

Parameters
__________
- Output file format: bigwig or bedgraph

Output
------
Two files with the first and the second eigenvector.

| 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>