comparison hicPlotViewpoint.xml @ 3:745e77f4e81e draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

2:bb82a2982d3d

<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" />

    <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:3200000-3300000' />
            <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>

3:745e77f4e81e

<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>plot interactions around a viewpoint</description>
    <macros>
        <token name="@BINARY@">hicPlotViewpoint</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <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" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: 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' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: 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:3200000-3300000' />
            <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[
Plot Viewpoint
==============

**hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data.
This plotting method allows to make long-range interactions more visible.

_________________

Usage
-----

This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.

_________________

Output
------

**hicPlotViewpoint** outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.

.. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
   :width: 80 %

_________________

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

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>