Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison 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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2:cdff00acac0f 3:5186eda61ca4
4 <token name="@BINARY@">hicMergeMatrixBins</token> 4 <token name="@BINARY@">hicMergeMatrixBins</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
10 ln -s '$matrix' input.npz.h5 &&
11
12 hicMergeMatrixBins 9 hicMergeMatrixBins
13 --matrix input.npz.h5 10 --matrix '$matrix_h5_cooler'
14 --numBins $numBins 11 --numBins $numBins
15 $runningWindow 12 $runningWindow
16 --outFileName ./out.npz.h5 13 --outFileName ./out.npz.h5
17 14
18 ]]> 15 ]]>
19 </command> 16 </command>
20 <inputs> 17 <inputs>
21 <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" /> 18 <expand macro='matrix_h5_cooler_macro' />
19
22 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> 20 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
23 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" /> 21 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
24 </inputs> 22 </inputs>
25 <outputs> 23 <outputs>
26 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/> 24 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
27 </outputs> 25 </outputs>
28 <tests> 26 <tests>
29 <test> 27 <test>
30 <param name="matrix" value="small_test_matrix.h5" /> 28 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
31 <param name="numBins" value="5" /> 29 <param name="numBins" value="5" />
32 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" /> 30 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
33 </test> 31 </test>
34 </tests> 32 </tests>
35 <help><![CDATA[ 33 <help><![CDATA[
42 40
43 Number of bins to merge = 10 41 Number of bins to merge = 10
44 42
45 100 kb * 10 = 1000 kb = 1 Mb 43 100 kb * 10 = 1000 kb = 1 Mb
46 44
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. 45 This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
46 to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but
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
48 difficult to interpret, especially if the read depth of the Hi-C data is not high.
48 49
49 Input 50 Input
50 ----- 51 -----
51 52
52 Parameters 53 Parameters