Mercurial > repos > crs4 > seal_galaxy
comparison seal-galaxy-cc1b1911/seal/read_sort.xml @ 0:244073d9abc1 draft default tip
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author | crs4 |
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date | Wed, 15 Oct 2014 09:41:10 -0400 |
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1 | |
2 <!-- | |
3 Copyright (C) 2011-2014 CRS4. | |
4 | |
5 This file is part of Seal. | |
6 | |
7 Seal is free software: you can redistribute it and/or modify it | |
8 under the terms of the GNU General Public License as published by the Free | |
9 Software Foundation, either version 3 of the License, or (at your option) | |
10 any later version. | |
11 | |
12 Seal is distributed in the hope that it will be useful, but | |
13 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY | |
14 or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License | |
15 for more details. | |
16 | |
17 You should have received a copy of the GNU General Public License along | |
18 with Seal. If not, see <http://www.gnu.org/licenses/>. | |
19 --> | |
20 | |
21 | |
22 <tool id="seal_read_sort" name="ReadSort" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4"> | |
23 <description>Sort reads with Hadoop</description> | |
24 <requirements> | |
25 <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement> | |
26 <requirement type="package" version="0.11">pydoop</requirement> | |
27 <requirement type="package" version="0.1.3">hadoop-galaxy</requirement> | |
28 </requirements> | |
29 <command> | |
30 #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path | |
31 hadoop_galaxy | |
32 --input $input_data | |
33 --output $output | |
34 --executable seal | |
35 read_sort | |
36 --annotations ${ref_path}.ann | |
37 --num-reducers $num_reducers | |
38 </command> | |
39 | |
40 <inputs> | |
41 <param name="input_data" type="data" format="pathset" label="Input data" /> | |
42 | |
43 <param name="reference" type="select" label="Reference (should be the same one used for alignment)"> | |
44 <options from_data_table="bwa_0510_indexes" /> | |
45 </param> | |
46 | |
47 <param name="num_reducers" | |
48 label="Number of reduce tasks" | |
49 type="integer" | |
50 value="90" | |
51 min="1" | |
52 /> | |
53 </inputs> | |
54 | |
55 <outputs> | |
56 <data name="output" format="pathset" /> | |
57 </outputs> | |
58 | |
59 <stdio> | |
60 <exit_code range="1:" level="fatal" /> | |
61 </stdio> | |
62 | |
63 <help> | |
64 ReadSort is a Hadoop-based program for sorting reads by alignment position. | |
65 For the full help see the `manual <http://biodoop-seal.sourceforge.net/read_sort_index.html>`_. | |
66 </help> | |
67 | |
68 </tool> |