Mercurial > repos > bgruening > hicexplorer_hicaverageregions
comparison hicAverageRegions.xml @ 2:4b6a36c18e5e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author | iuc |
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date | Wed, 11 Mar 2020 17:05:58 -0400 |
parents | d4aa0255c1eb |
children | 03d7978293fe |
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1:d4aa0255c1eb | 2:4b6a36c18e5e |
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4 <token name="@BINARY@">hicAverageRegions</token> | 4 <token name="@BINARY@">hicAverageRegions</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 | 9 |
10 | 10 |
11 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && | 11 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && |
12 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' | 12 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' |
13 | 13 |
14 --regions '$regions' | 14 --regions '$regions' |
25 <inputs> | 25 <inputs> |
26 <expand macro='matrix_h5_cooler_macro' /> | 26 <expand macro='matrix_h5_cooler_macro' /> |
27 <param argument="--regions" type="data" format='bed' | 27 <param argument="--regions" type="data" format='bed' |
28 label="Regions to average" | 28 label="Regions to average" |
29 help="BED file which stores a list of regions that are summed and averaged."/> | 29 help="BED file which stores a list of regions that are summed and averaged."/> |
30 | 30 |
31 <conditional name="rangeFormat_conditional"> | 31 <conditional name="rangeFormat_conditional"> |
32 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> | 32 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
33 <option value="optionGenomicUnits">Range in genomic units</option> | 33 <option value="optionGenomicUnits">Range in genomic units</option> |
34 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> | 34 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> |
35 </param> | 35 </param> |
78 <help><![CDATA[ | 78 <help><![CDATA[ |
79 | 79 |
80 Average regions | 80 Average regions |
81 =============== | 81 =============== |
82 | 82 |
83 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. | 83 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, TAD boundaries for instance, between samples. |
84 | 84 |
85 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. | 85 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. |
86 | 86 |
87 Use the output to plot the average with hicPlotAverageRegions. | 87 Use the output to plot the average with hicPlotAverageRegions. |
88 | 88 |