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comparison seal-galaxy-cc1b1911/seal/recab_table.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_recab_table" name="Recab Table" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
23 <description>Calculate a base quality recalibration table on 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
30 <command interpreter="python">
31 recab_table_galaxy.py
32 $input_data
33 $output1
34
35 #if $dbsnp.db_source == "history":
36 $dbsnp.ownFile
37 #else:
38 ${dbsnp.built-inFile.fields.path}
39 #end if
40
41 $num_reducers
42
43 #if $default_rg:
44 -D seal.recab.rg-covariate.default-rg=$default_rg
45 #end if
46
47 #if $smoothing:
48 -D seal.recab.smoothing=$smoothing
49 #end if
50
51 #if $max_qscore:
52 -D seal.recab.max-qscore=$max_qscore
53 #end if
54 </command>
55
56 <inputs>
57 <param name="input_data" type="data" format="pathset" label="Input data" />
58 <param name="input_format" type="select" label="Input format" default="sam">
59 <option value="sam" />
60 <option value="bam" />
61 </param>
62
63 <conditional name="dbsnp">
64 <param name="db_source" type="select" label="Select database of known variation sites">
65 <option value="built-in">Select a different built-in database</option>
66 <option value="history">Use a database (vcf format) from my history</option>
67 </param>
68
69 <when value="built-in">
70 <param name="built-inFile" type="select" label="Select a built-in database">
71 <options from_data_table="variant_tables"/>
72 </param>
73 </when>
74
75 <when value="history">
76 <param name="ownFile" type="data" format="vcf" label="Select a database from history"/>
77 </when>
78 </conditional>
79
80
81 <param name="num_reducers"
82 label="Number of reduce tasks"
83 type="integer"
84 value="90"
85 min="1"
86 />
87
88 <!-- recab-specific parameters -->
89 <param name="default_rg"
90 label="Default read group"
91 type="text"
92 help="Read group to assign to mappings without an RG tag. This value is mandatory if your data includes mappings that do not have a read group tag (RG) Seal RecabTable property: seal.recab.rg-covariate.default-rg."
93 />
94 <param name="smoothing"
95 label="Smoothing"
96 type="integer"
97 value="0"
98 help="Smoothing parameter for empirical quality calculation. Seal RecabTable property: seal.recab.smoothing."
99 min="0"
100 />
101 <param name="max_qscore"
102 label="Max quality score"
103 type="integer"
104 value="40"
105 min="1"
106 help="Upper limit for the empirical quality scores. Seal RecabTable property: seal.recab.max-qscore."
107 />
108 </inputs>
109
110 <outputs>
111 <data name="output1" format="csv" />
112 </outputs>
113
114 <stdio>
115 <exit_code range="1:" level="fatal" />
116 </stdio>
117
118 <help>
119 RecabTable is a Hadoop program to calculate a table of base qualities for all values of a given set of factors. It computes a result equivalent to the GATK CountCovariatesWalker.
120 For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/recab_table_index.html&gt;`_.
121 </help>
122 </tool>