Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison hicMergeMatrixBins.xml @ 2:cdff00acac0f draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:33:36 -0500
parents a1cf508bff84
children 5186eda61ca4
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1:d965ec46db1e 2:cdff00acac0f
32 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" /> 32 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <help><![CDATA[ 35 <help><![CDATA[
36 36
37 **What it does** 37 Change matrix resolution
38 ========================
38 39
39 Merges neighboring bins in a Hi-C matrix. 40 ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb
41 contact matrix a 1000 kb one:
40 42
43 Number of bins to merge = 10
44
45 100 kb * 10 = 1000 kb = 1 Mb
46
47 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.
48
49 Input
50 -----
51
52 Parameters
53 __________
54 - contact matrix to change the resolution on
55 - Number of bins to merge
56 - running window
57
58 Output
59 ------
60
61 A contact matrix with the resolution ``original resolution * number of bins``.
62
63 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
64
65 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
41 ]]></help> 66 ]]></help>
42 <expand macro="citations" /> 67 <expand macro="citations" />
43 </tool> 68 </tool>