comparison hicMergeMatrixBins.xml @ 3:5186eda61ca4 draft

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

2:cdff00acac0f

        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$matrix' input.npz.h5 &&

        hicMergeMatrixBins
            --matrix input.npz.h5
            --numBins $numBins
            $runningWindow
            --outFileName ./out.npz.h5

]]>
    </command>
    <inputs>
        <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" />
        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="small_test_matrix.h5" />
            <param name="numBins" value="5" />
            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
        </test>
    </tests>
    <help><![CDATA[

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it difficult to interpret, especially if the read depth of the Hi-C data is not high.

Input
-----

Parameters

3:5186eda61ca4

        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        hicMergeMatrixBins
            --matrix '$matrix_h5_cooler'
            --numBins $numBins
            $runningWindow
            --outFileName ./out.npz.h5

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
            <param name="numBins" value="5" />
            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
        </test>
    </tests>
    <help><![CDATA[

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but 
to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it 
difficult to interpret, especially if the read depth of the Hi-C data is not high.

Input
-----

Parameters