Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate hicMergeMatrixBins.xml @ 3:5186eda61ca4 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:16:29 -0500
parents cdff00acac0f
children d04398893232
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a1cf508bff84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Merges bins from a Hi-C matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicMergeMatrixBins</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 hicMergeMatrixBins
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10 --matrix '$matrix_h5_cooler'
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11 --numBins $numBins
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12 $runningWindow
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13 --outFileName ./out.npz.h5
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro='matrix_h5_cooler_macro' />
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19
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20 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
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21 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
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22 </inputs>
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23 <outputs>
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24 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
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25 </outputs>
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26 <tests>
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27 <test>
3
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28 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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29 <param name="numBins" value="5" />
a1cf508bff84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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30 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
a1cf508bff84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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31 </test>
a1cf508bff84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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32 </tests>
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33 <help><![CDATA[
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34
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35 Change matrix resolution
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36 ========================
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cdff00acac0f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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38 ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb
cdff00acac0f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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39 contact matrix a 1000 kb one:
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41 Number of bins to merge = 10
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43 100 kb * 10 = 1000 kb = 1 Mb
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3
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45 This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
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46 to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but
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47 to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it
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48 difficult to interpret, especially if the read depth of the Hi-C data is not high.
2
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49
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50 Input
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51 -----
0
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53 Parameters
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54 __________
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55 - contact matrix to change the resolution on
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56 - Number of bins to merge
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57 - running window
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59 Output
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60 ------
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61
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62 A contact matrix with the resolution ``original resolution * number of bins``.
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64 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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65
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66 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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67 ]]></help>
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68 <expand macro="citations" />
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69 </tool>