Mercurial > repos > bgruening > hicexplorer_hicaverageregions

comparison hicAverageRegions.xml @ 2:4b6a36c18e5e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:05:58 -0400
parents d4aa0255c1eb
children 03d7978293fe
comparison
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1:d4aa0255c1eb 2:4b6a36c18e5e
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