comparison hicCorrectMatrix.xml @ 14:1e622e371512 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"

13:9949f055db84

<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>run Imakaev's iterative correction over a Hi-C contact matrix.</description>
    <macros>
        <token name="@BINARY@">hicCorrectMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <help><![CDATA[

Hi-C contact matrix correction
==============================

**hicCorrectMatrix** runs Imakaev's iterative correction, described in `Imakaev et al. (2012)`_, over a Hi-C matrix. For the matrix correction to be efficient,
it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length
chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here.

**Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.

14:1e622e371512

<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>run a Hi-C matrix correction algorithm</description>
    <macros>
        <token name="@BINARY@">hicCorrectMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <help><![CDATA[

Hi-C contact matrix correction
==============================

**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,
it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length
chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here.

**Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.