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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="dist_bcl2qseq" name="Dist Bcl2Qseq" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
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23 <description>Convert Illumina bcl files to qseq 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>
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31 hadoop_galaxy
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32 --executable seal
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33 --input $input_data
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34 --output $output1
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35 bcl2qseq
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36 #if $advanced.control == 'show'
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37 #if $advanced.bcl2qseq_bin:
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38 --bclToQseq-path $advanced.bcl2qseq_bin
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39 #end if
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40
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41 #if $advanced.additional_ld_path
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42 --append-ld-library-path $advanced.additional_ld_path
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43 #end if
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44
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45 #if $advanced.ignore_missing_bcl
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46 --ignore-missing-bcl
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47 #end if
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48
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49 #if $advanced.ignore_missing_control
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50 --ignore-missing-control
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51 #end if
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52
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53 #if $advanced.exclude_controls
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54 --exclude-controls
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55 #end if
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56
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57 #if $advanced.no_eamss
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58 --no-eamss
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59 #end if
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60 #end if
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61 </command>
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62
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63 <inputs>
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64 <param name="input_data" type="data" format="pathset" label="Source data set"/>
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65 <conditional name="advanced">
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66 <param name="control" type="select" label="Advanced controls" default="hide">
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67 <option value="hide">Hide</option>
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68 <option value="show">Show</option>
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69 </param>
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70 <when value="show">
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71 <param name="ignore_missing_bcl"
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72 type="boolean" default="false"
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73 label="Interpret missing *.bcl files as a base calling of '.'"
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74 />
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75 <param name="ignore_missing_control"
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76 type="boolean" default="false"
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77 label="Don't throw an error when *.control files are missing"
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78 />
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79 <param name="exclude_controls"
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80 type="boolean" default="false"
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81 label="Do not include clusters that are used as controls"
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82 />
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83 <param name="no_eamss"
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84 type="boolean" default="false"
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85 label="Do not apply the EAMSS masking on the quality values"
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86 />
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87 <param name="bcl2qseq_bin"
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88 type="text"
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89 default=""
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90 size="80"
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91 label="Full path to bclToQseq binary (needed only if the executable isn't in the PATH)"
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92 />
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93 <param name="additional_ld_path"
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94 type="text" default="" size="80"
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95 label="paths to append to the value of LD_LIBRARY_PATH"
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96 />
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97 </when>
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98 </conditional>
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99 </inputs>
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100
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101 <outputs>
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102 <data name="output1" format="pathset" label="Qseq" />
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103 </outputs>
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104
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105 <stdio>
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106 <exit_code range="1:" level="fatal" />
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107 </stdio>
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108
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109 <help>
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110 This is a Pydoop-based distributed version of Illumina's bclToQseq tool.
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111 </help>
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112 </tool>
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