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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 |
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modified:
hicMergeMatrixBins.xml macros.xml |
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added:
static/images/SRR027956.svg static/images/SRR0279XX_perChr_eigenvector1.png static/images/diagnostic_plot.png static/images/hicCorrelate_pearson.png static/images/hicCorrelate_pearson_scatter.png static/images/hicCorrelate_spearman.png static/images/hicCorrelate_spearman_scatter.png static/images/hicPlotDistVsCounts_result1.png static/images/hicPlotDistVsCounts_result2.png static/images/hicQC.png static/images/master_TADs_plot.png static/images/z-score.svg |
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| diff -r d965ec46db1e -r cdff00acac0f hicMergeMatrixBins.xml --- a/hicMergeMatrixBins.xml Mon Nov 27 11:13:54 2017 -0500 +++ b/hicMergeMatrixBins.xml Sat Dec 16 16:33:36 2017 -0500 |
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| @@ -34,10 +34,35 @@ </tests> <help><![CDATA[ -**What it does** +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 +----- -Merges neighboring bins in a Hi-C matrix. +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> |
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| diff -r d965ec46db1e -r cdff00acac0f macros.xml --- a/macros.xml Mon Nov 27 11:13:54 2017 -0500 +++ b/macros.xml Sat Dec 16 16:33:36 2017 -0500 |
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| @@ -21,7 +21,7 @@ </xml> <xml name="colormap"> - <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> + <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu">RdYlBu</option> <option value="Accent">Accent</option> <option value="Spectral">Spectral</option> |
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| diff -r d965ec46db1e -r cdff00acac0f static/images/SRR027956.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/SRR027956.svg Sat Dec 16 16:33:36 2017 -0500 |
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