view hicMergeMatrixBins.xml @ 0:a1cf508bff84 draft

planemo upload for repository commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:08:52 -0400
children cdff00acac0f
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<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Merges bins from a Hi-C matrix</description>
        <token name="@BINARY@">hicMergeMatrixBins</token>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

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

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

        <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" />
        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
            <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" />

**What it does**

Merges neighboring bins in a Hi-C matrix.

    <expand macro="citations" />