comparison seal-galaxy-cc1b1911/seal/merge_alignments.xml @ 0:244073d9abc1 draft default tip

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author crs4
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_merge_alignments" name="Merge Alignments" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
23 <description>Merge a pathset of part-files of alignments into a single well-formatted SAM file</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 interpreter="python">
30 #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
31 merge_alignments.py
32 $input_data
33 $output
34
35 --annotations ${ref_path}.ann
36 --sort-order $sort_order
37
38 #if $compute_md5:
39 --md5
40 #end if
41
42 #if $assembly:
43 --sq-assembly "$assembly"
44 #end if
45
46 #if $rg.set_rg == 'true':
47 --rg_cn "$rg.rg_cn"
48 --rg_dt "$rg.rg_dt"
49 --rg_id "$rg.rg_id"
50 --rg_lb "$rg.rg_lb"
51 --rg_pl "$rg.rg_pl"
52 --rg_pu "$rg.rg_pu"
53 --rg_sm "$rg.rg_sm"
54 #end if
55 </command>
56
57 <inputs>
58 <param name="input_data" type="data" format="pathset" label="Input data" />
59
60 <param name="reference" type="select" label="Reference (should be the same one used for alignment)">
61 <options from_data_table="bwa_0510_indexes" />
62 </param>
63
64 <param name="sort_order" type="select" default="coordinate">
65 <option value="coordinate">Coordinate</option>
66 <option value="read_id">Read ID</option>
67 <option value="unsorted">Unsorted</option>
68 </param>
69 <param name="compute_md5" type="boolean" checked="false" label="Whether to compute the MD5 checksums of the reference contigs" />
70 <param name="assembly" type="text" label="Genome assembly identifier (@SQ AS:XXX tag)" />
71
72 <conditional name="rg">
73 <param name="set_rg" type="boolean" checked="false" label="Set a Read Group line" truevalue="true" falsevalue="false" />
74
75 <when value="true">
76 <param name="rg_cn" type="text" label="Read group center" />
77 <param name="rg_dt" type="text" label="Read group date" />
78 <param name="rg_id" type="text" label="Read group id" />
79 <param name="rg_lb" type="text" label="Read group library" />
80 <param name="rg_pl" type="text" label="Read group platform" />
81 <param name="rg_pu" type="text" label="Read group platform unit" />
82 <param name="rg_sm" type="text" label="Read group sample" />
83 </when>
84 </conditional>
85 </inputs>
86
87 <outputs>
88 <data name="output" format="sam" />
89 </outputs>
90
91 <stdio>
92 <exit_code range="1:" level="fatal" />
93 </stdio>
94
95 <help>
96 ReadSort is a Hadoop-based program for sorting reads by alignment position.
97 For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/read_sort_index.html&gt;`_.
98 </help>
99
100 </tool>