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1 <!--annotateGenes - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 Copyright (C) 2015 Institut Curie
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3
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4 This program is free software: you can redistribute it and/or modify
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5 it under the terms of the GNU General Public License as published by
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6 the Free Software Foundation, either version 3 of the License, or
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7 (at your option) any later version.
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8
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9 This program is distributed in the hope that it will be useful,
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10 but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 GNU General Public License for more details.
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13
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14 You should have received a copy of the GNU General Public License
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15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
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16 <tool id="extractCentralRegions" name="Extract regions around peak maxima for a .bed file with peak coordinates" version="1.0">
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17 <description> </description>
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18 <requirements>
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19 <container type="docker">institutcuriengsintegration/extractcentralregions:1.0</container>
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20 </requirements>
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21 <command interpreter="perl">extractCentralRegions.pl -f $inputfile -l $left -o $output -head $has_header
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22 </command>
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23 <inputs>
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24
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25 <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed,txt"/>
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26 <param name="has_header" type="select" label="Your data file has a header?">
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27 <option value="0" selected="true">No</option>
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28 <option value="1">Yes</option>
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29 </param>
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30 <param name="left" type="integer" label="Legth of the central region" value="300"/>
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31 </inputs>
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32 <outputs>
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33 <data name="output" format="bed" label="central regions for ${inputfile.name}"/>
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34 </outputs>
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35 <help>
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36 **What it does**
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37
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38 This tool extract central regions of ChIP-seq peaks
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39
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40 </help>
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41 </tool>
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