annotate hicPCA.xml @ 3:ea50f7bba657 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457

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

        hicPCA --matrix '$matrix_h5_cooler'
       
        --outputFileName pca1.$outputFormat pca2.$outputFormat
        --format $outputFormat
        
        && mv pca1.$outputFormat pca1
        && mv pca2.$outputFormat pca2

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name='outputFormat' type='select' label="Output file format">
            <option value='bigwig' selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

    </inputs>
    <outputs>
       
        <data name="pca1" from_work_dir="pca1" format="bigwig">
            <filter>outputFormat == 'bigwig'</filter>
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>
        <data name="pca2" from_work_dir="pca2" format="bigwig">
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>

        
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
            <param name="outputFormat" value="bedgraph" />
            <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
            <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>

            <param name="outputFormat" value="bigwig" />
            <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
            <output name="pca2" file="pca2.bw" ftype="bigwig" 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>