annotate hicPCA.xml @ 0:61165fbb020d draft

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

<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'
       
        #if $outputFormat == 'bigwig'
            --outputFileName 'pca1.bigwig' 'pca2.bigwig'
            --format bigwig
        #elif $outputFormat == 'bedgraph'
            --outputFileName 'pca1.bedgraph' 'pca2.bedgraph'
            --format bedgraph
        #end if

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

    </inputs>
    <outputs>
       
        <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig">
            <filter>outputFormat == 'bigwig'</filter>
        </data>
        <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig">
            <filter>outputFormat == 'bigwig'</filter>
        </data>

        <data name="pca1_bedgraph" from_work_dir="pca1.bedgraph" format="bedgraph">
            <filter>outputFormat == 'bedgraph'</filter>
        </data>
        <data name="pca2_bedgraph" from_work_dir="pca2.bedgraph" format="bedgraph">
            <filter>outputFormat == 'bedgraph'</filter>
        </data>
        
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
            <param name="outputFormat" value="bedgraph" />
            <output name="pca1_bedgraph" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
            <output name="pca2_bedgraph" 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_bw" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
            <output name="pca2_bw" 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>