annotate hicTransform.xml @ 2:3106dcd651f5 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1">
    <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
    <macros>
        <token name="@BINARY@">hicTransform</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[


        hicTransform --matrix '$matrix_h5_cooler'
        --method all
        --outFileName matrix.$outputFormat
        && mv obs_exp_matrix.$outputFormat obs_exp_matrix
        && mv pearson_matrix.$outputFormat pearson_matrix
        && mv covariance_matrix.$outputFormat covariance_matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name='outputFormat' type='select' label="Output file format">
            <option value='h5'>HiCExplorer format</option>
            <option value="cool">cool</option>
        </param>

    </inputs>
    <outputs>
        <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5">
            <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
        <data name="pearson" from_work_dir="pearson_matrix" format="h5">
            <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
        <data name="covariance" from_work_dir="covariance_matrix" format="h5">
            <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
            <param name="outputFormat" value="h5" />
            <output name="obs_exp" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
            <output name="pearson" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
            <output name="covariance" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
            <param name="outputFormat" value="cool" />
            <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
            <output name="pearson" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
            <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Transformation of matrix for plotting
=====================================
`hicTransform` computes three matrices: an observed/expected matrix based on it a
pearson correlation matrix and based on it a covariance matrix. These three matrices
can be used with `hicPlotMatrix` for an A / B compartment analysis.

Input
-----
- the matrix to be transformed

Parameters
__________
- Output file format: h5 or cool

Output
------
- observed/expected matrix
- pearson correlation matrix 
- covariance matrix.

| 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>