Mercurial > repos > bgruening > hicexplorer_hicaverageregions
comparison hicAverageRegions.xml @ 0:f7c0aedd4be3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 15:21:06 -0500 |
parents | |
children | d4aa0255c1eb |
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-1:000000000000 | 0:f7c0aedd4be3 |
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1 <tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
2 <description>sums Hi-C contacts around given reference points and computes their average.</description> | |
3 <macros> | |
4 <token name="@BINARY@">hicAverageRegions</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 | |
10 | |
11 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && | |
12 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' | |
13 | |
14 --regions '$regions' | |
15 #if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits': | |
16 --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' | |
17 #else: | |
18 --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' | |
19 #end if | |
20 --outFileName output_matrix.npz | |
21 | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <expand macro='matrix_h5_cooler_macro' /> | |
26 <param argument="--regions" type="data" format='bed' | |
27 label="Regions to average" | |
28 help="BED file which stores a list of regions that are summed and averaged."/> | |
29 | |
30 <conditional name="rangeFormat_conditional"> | |
31 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> | |
32 <option value="optionGenomicUnits">Range in genomic units</option> | |
33 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> | |
34 </param> | |
35 <when value="optionGenomicUnits"> | |
36 <param name="upstreamRange" type="integer" value="" label="Upstream range"/> | |
37 <param name="downstreamRange" type="integer" value="" label="Downstream range"/> | |
38 </when> | |
39 <when value="optionBinUnits"> | |
40 <param name="upstreamRange" type="integer" value="" label="Upstream range"/> | |
41 <param name="downstreamRange" type="integer" value="" label="Downstream range"/> | |
42 </when> | |
43 </conditional> | |
44 </inputs> | |
45 <outputs> | |
46 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/> | |
47 </outputs> | |
48 <tests> | |
49 <test> | |
50 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | |
51 <param name="regions" value="hicAverageRegions/regions.bed" /> | |
52 <conditional name="rangeFormat_conditional"> | |
53 <param name="rangeFormat_selector" value='optionGenomicUnits'/> | |
54 <param name="upstreamRange" value='100000'/> | |
55 <param name="downstreamRange" value='100000'/> | |
56 </conditional> | |
57 | |
58 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" /> | |
59 </test> | |
60 <test> | |
61 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | |
62 <param name="regions" value="hicAverageRegions/regions.bed" /> | |
63 <conditional name="rangeFormat_conditional"> | |
64 <param name="rangeFormat_selector" value='optionBinUnits'/> | |
65 <param name="upstreamRange" value='100'/> | |
66 <param name="downstreamRange" value='100'/> | |
67 </conditional> | |
68 | |
69 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" /> | |
70 </test> | |
71 </tests> | |
72 <help><![CDATA[ | |
73 | |
74 Average regions | |
75 =============== | |
76 | |
77 This tool sums Hi-C contacts around given reference points and computes their average. This tool is useful to detect differences at certain reference points as for example TAD boundaries between samples. | |
78 | |
79 WARNING: This tool can only be used with fixed bin size Hi-C matrices. No guarantees how and if it works on restriction site interaction matrices. | |
80 | |
81 Use the output to plot the average with hicPlotAverageRegions. | |
82 | |
83 _________________ | |
84 | |
85 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | |
86 | |
87 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
88 ]]></help> | |
89 <expand macro="citations" /> | |
90 </tool> |