Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate hicMergeMatrixBins.xml @ 5:1111999ae668 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:19:56 -0500
parents 2a62d67cab68
children 0c6d98e9c6e8
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1111999ae668 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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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 $runningWindow
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13 --outFileName matrix.$outputFormat
1111999ae668 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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14 && mv matrix.$outputFormat matrix
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16 ]]>
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17 </command>
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18 <inputs>
3
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19 <expand macro='matrix_h5_cooler_macro' />
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20
0
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21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
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22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
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23 <param name='outputFormat' type='select' label="Output file format">
1111999ae668 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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24 <option value='h5' selected='true'>HiCExplorer format</option>
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25 <option value="cool">cool</option>
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26 </param>
0
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27 </inputs>
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28 <outputs>
5
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29 <data name="outFileName" from_work_dir="matrix" format="h5">
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30 <change_format>
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31 <when input="outputFormat" value="cool" format="cool" />
1111999ae668 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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32 </change_format>
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33 </data>
0
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34 </outputs>
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35 <tests>
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36 <test>
3
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37 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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38 <param name="numBins" value="5" />
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39 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43
2
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44 Change matrix resolution
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45 ========================
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47 ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb
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48 contact matrix a 1000 kb one:
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49
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50 Number of bins to merge = 10
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52 100 kb * 10 = 1000 kb = 1 Mb
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53
3
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54 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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55 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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56 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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57 difficult to interpret, especially if the read depth of the Hi-C data is not high.
2
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59 Input
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60 -----
0
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61
2
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62 Parameters
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63 __________
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64 - contact matrix to change the resolution on
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65 - Number of bins to merge
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66 - running window
0
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67
2
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68 Output
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69 ------
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70
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71 A contact matrix with the resolution ``original resolution * number of bins``.
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72
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73 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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75 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
0
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>