Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins
view hicMergeMatrixBins.xml @ 4:8cad169bde4c draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
author | iuc |
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date | Tue, 02 Jan 2018 10:15:37 -0500 |
parents | 5186eda61ca4 |
children | d04398893232 |
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<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>Merges bins from a Hi-C matrix</description> <macros> <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[ Change matrix resolution ======================== ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb contact matrix a 1000 kb one: 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 __________ - contact matrix to change the resolution on - Number of bins to merge - running window Output ------ A contact matrix with the resolution ``original resolution * number of bins``. | 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>