Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 14:1e622e371512 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 19:39:47 -0500
parents 9949f055db84
children c543c41377dd
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13:9949f055db84 14:1e622e371512
1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>run Imakaev's iterative correction over a Hi-C contact matrix.</description> 2 <description>run a Hi-C matrix correction algorithm</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCorrectMatrix</token> 4 <token name="@BINARY@">hicCorrectMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
210 <help><![CDATA[ 210 <help><![CDATA[
211 211
212 Hi-C contact matrix correction 212 Hi-C contact matrix correction
213 ============================== 213 ==============================
214 214
215 **hicCorrectMatrix** runs Imakaev's iterative correction, described in `Imakaev et al. (2012)`_, over a Hi-C matrix. For the matrix correction to be efficient, 215 **hicCorrectMatrix** runs Imakaev's iterative correction, described in `Imakaev et al. (2012)`_, or Knight-Ruiz correction over a Hi-C matrix. For the matrix correction to be efficient,
216 it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length 216 it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length
217 chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here. 217 chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here.
218 218
219 **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix. 219 **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.
220 220