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2 <!--
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3 Copyright (C) 2011-2014 CRS4.
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4
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5 This file is part of Seal.
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6
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7 Seal is free software: you can redistribute it and/or modify it
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8 under the terms of the GNU General Public License as published by the Free
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9 Software Foundation, either version 3 of the License, or (at your option)
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10 any later version.
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11
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12 Seal is distributed in the hope that it will be useful, but
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13 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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14 or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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15 for more details.
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16
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17 You should have received a copy of the GNU General Public License along
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18 with Seal. If not, see <http://www.gnu.org/licenses/>.
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19 -->
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20
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21
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22 <tool id="seal_read_sort" name="ReadSort" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
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23 <description>Sort reads with Hadoop</description>
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24 <requirements>
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25 <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement>
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26 <requirement type="package" version="0.11">pydoop</requirement>
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27 <requirement type="package" version="0.1.3">hadoop-galaxy</requirement>
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28 </requirements>
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29 <command>
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30 #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
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31 hadoop_galaxy
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32 --input $input_data
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33 --output $output
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34 --executable seal
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35 read_sort
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36 --annotations ${ref_path}.ann
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37 --num-reducers $num_reducers
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38 </command>
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39
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40 <inputs>
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41 <param name="input_data" type="data" format="pathset" label="Input data" />
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42
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43 <param name="reference" type="select" label="Reference (should be the same one used for alignment)">
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44 <options from_data_table="bwa_0510_indexes" />
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45 </param>
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46
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47 <param name="num_reducers"
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48 label="Number of reduce tasks"
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49 type="integer"
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50 value="90"
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51 min="1"
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52 />
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53 </inputs>
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54
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55 <outputs>
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56 <data name="output" format="pathset" />
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57 </outputs>
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58
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59 <stdio>
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60 <exit_code range="1:" level="fatal" />
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61 </stdio>
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62
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63 <help>
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64 ReadSort is a Hadoop-based program for sorting reads by alignment position.
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65 For the full help see the `manual <http://biodoop-seal.sourceforge.net/read_sort_index.html>`_.
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66 </help>
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67
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68 </tool>
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