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1
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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_recab_table" name="Recab Table" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
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23 <description>Calculate a base quality recalibration table on 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
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30 <command interpreter="python">
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31 recab_table_galaxy.py
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32 $input_data
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33 $output1
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34
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35 #if $dbsnp.db_source == "history":
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36 $dbsnp.ownFile
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37 #else:
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38 ${dbsnp.built-inFile.fields.path}
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39 #end if
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40
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41 $num_reducers
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42
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43 #if $default_rg:
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44 -D seal.recab.rg-covariate.default-rg=$default_rg
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45 #end if
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46
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47 #if $smoothing:
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48 -D seal.recab.smoothing=$smoothing
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49 #end if
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50
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51 #if $max_qscore:
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52 -D seal.recab.max-qscore=$max_qscore
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53 #end if
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54 </command>
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55
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56 <inputs>
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57 <param name="input_data" type="data" format="pathset" label="Input data" />
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58 <param name="input_format" type="select" label="Input format" default="sam">
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59 <option value="sam" />
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60 <option value="bam" />
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61 </param>
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62
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63 <conditional name="dbsnp">
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64 <param name="db_source" type="select" label="Select database of known variation sites">
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65 <option value="built-in">Select a different built-in database</option>
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66 <option value="history">Use a database (vcf format) from my history</option>
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67 </param>
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68
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69 <when value="built-in">
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70 <param name="built-inFile" type="select" label="Select a built-in database">
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71 <options from_data_table="variant_tables"/>
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72 </param>
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73 </when>
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74
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75 <when value="history">
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76 <param name="ownFile" type="data" format="vcf" label="Select a database from history"/>
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77 </when>
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78 </conditional>
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79
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80
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81 <param name="num_reducers"
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82 label="Number of reduce tasks"
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83 type="integer"
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84 value="90"
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85 min="1"
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86 />
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87
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88 <!-- recab-specific parameters -->
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89 <param name="default_rg"
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90 label="Default read group"
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91 type="text"
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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."
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93 />
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94 <param name="smoothing"
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95 label="Smoothing"
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96 type="integer"
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97 value="0"
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98 help="Smoothing parameter for empirical quality calculation. Seal RecabTable property: seal.recab.smoothing."
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99 min="0"
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100 />
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101 <param name="max_qscore"
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102 label="Max quality score"
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103 type="integer"
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104 value="40"
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105 min="1"
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106 help="Upper limit for the empirical quality scores. Seal RecabTable property: seal.recab.max-qscore."
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107 />
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108 </inputs>
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109
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110 <outputs>
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111 <data name="output1" format="csv" />
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112 </outputs>
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113
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114 <stdio>
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115 <exit_code range="1:" level="fatal" />
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116 </stdio>
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117
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118 <help>
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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.
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120 For the full help see the `manual <http://biodoop-seal.sourceforge.net/recab_table_index.html>`_.
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121 </help>
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122 </tool>
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