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1 <tool id="preprocess" name="Data Normalization" force_history_refresh="True" version="0.1.0">
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2 <requirements>
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3 <requirement type="set_environment">R_SCRIPT_PATH</requirement>
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4 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 preprocess.py
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8 -s '$summary'
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9 -p '$__new_file_path__'
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10 -c '$inputcdffull.name'
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11 -f '$inputufl.name'
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12 -g '$inputugp.name'
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13 -a '$inputacs.name'
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14 -d '$inputcdffull'
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15 -v '$inputufl'
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16 -h '$inputugp'
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17 -b '$inputacs'
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18 #if $settings.settingsType == "tumor":
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19 -t '$tumorcsv'
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20 #end if
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21 #if $settings.settingsType == "standard":
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22 -t 'none'
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23 #end if
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24 -y '$settings.settingsType'
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25 -o '$outputgraph'
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26 -z '$zipfigures'
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27 -k '$outputlog'
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28 -l '$log'
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29 -u '$__user_id__'
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30 #for $input in $inputs
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31 -i "${input}"
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32 -n "${input.name}
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33 #end for
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34 </command>
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35 <inputs>
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36 <param name="inputs" type="data" format="cel" multiple="True" label="Cel files dataset" help="Cel files dataset previously uploaded with the Multiple File Datasets tool."/>
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37 <param name="inputcdffull" type="data" format="cdf" label="cdf file" help=".cdf file name must comply with the following format : < chiptype >,< tag >.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf)." />
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38 <param name="inputufl" type="data" format="ufl" label="ufl file" help=".ufl file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl)."/>
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39 <param name="inputugp" type="data" format="ugp" label="ugp file" help=".ugp file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp)."/>
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40 <param name="inputacs" type="data" format="acs" label="acs file" help=".acs file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs)."/>
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41 <conditional name="settings">
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42 <param name="settingsType" type="select" label="Reference">
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43 <option value="standard">Study without reference</option>
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44 <option value="tumor">Normal-tumor study with TumorBoost</option>
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45 </param>
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46 <when value="standard" />
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47 <when value="tumor">
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48 <param name="tumorcsv" type="data" format="csv" label="TumorBoost csv file" help="Normal-tumor csv file. See below for more information."/>
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49 </when>
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50 </conditional>
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51 <!--param name="outputgraph" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output figures" /-->
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52 <!--param name="outputlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output log" /-->
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53 <param name="outputgraph" type="select" label="Output figures">
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54 <option value="TRUE">Yes</option>
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55 <option value="FALSE">No</option>
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56 </param>
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57 <param name="outputlog" type="select" label="Output log">
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58 <option value="TRUE">Yes</option>
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59 <option value="FALSE">No</option>
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60 </param>
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61 <!--param name="chipType" type="text" label="chipType" /-->
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62 <!--param name="workspace" type="text" label="Workspace"/-->
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63 </inputs>
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64
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65 <outputs>
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66 <!-- Would like to make this hidden or not appear all together, but
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67 variable outputs require a primary dataset. If hidden refresh
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68 doesn't occur.
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69 -->
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70 <data format="dsf" name="summary" label="Dataset summary file of ${input.name} " />
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71 <data format="zip" name="zipfigures" label="figures of normalization of ${input.name}">
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72 <filter>outputgraph == "TRUE"</filter>
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73 </data>
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74 <data format="log" name="log" label="log of normalization of ${input.name}">
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75 <filter>outputlog == "TRUE"</filter>
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76 </data>
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77 </outputs>
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78
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79 <stdio>
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80 <exit_code range="1:" level="fatal" description="See logs for more details" />
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81 </stdio>
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82
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83 <help>
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84
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85 **What it does**
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86
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87 This preprocessing step consists in a correction of biological and technical biaises due to the experiment. Raw data from Affymetrix arrays are provided in different CEL files. These data must be normalized before statistical analysis.
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88 The pre-processing is proposed as a wrapper of aroma.* packages (using CRMAv2 and TumorBoost when appropriate). Note that this implies that the pre-processing step is only available for Affymetrix arrays.
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89
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90 -----
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91
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92 **Chip file naming conventions**
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93
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94 Chip filenames must strictly follow the following rules :
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95
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96 - *.cdf* filename must comply with the following format : < chiptype >,< tag >.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf). Note the use of a comma (not a point) between <chiptype> and the tag "Full".
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97
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98 - *.ufl* filename must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl).
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99
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100 - *.ugp* filename must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp).
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101
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102 - *.acs* file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs).
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103
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104 -----
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105
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106 **Normal-tumor study with TumorBoost**
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107
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108 In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided :
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109
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110 - The first column contains the names of the files corresponding to normal samples of the dataset.
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111
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112 - The second column contains the names of the tumor samples files.
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113
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114 - Column names of these two columns are respectively normal and tumor.
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115
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116 - Columns are separated by a comma.
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117
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118 - *Extensions of the files (.CEL for example) should be removed*
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119
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120
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121
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122 **Example**
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123
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124 Let 6 .cel files in the dataset studied (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
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125
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126 patient1_normal.cel
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127 patient1_tumor.cel
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128 patient2_normal.cel
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129 patient2_tumor.cel
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130 patient3_normal.cel
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131 patient3_tumor.cel
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132
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133
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134 The csv file should look like this ::
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135
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136 normal,tumor
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137 patient1_normal,patient1_tumor
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138 patient2_normal,patient2_tumor
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139 patient3_normal,patient3_tumor
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140
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141
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142 -----
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143
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144 **Citation**
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145
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146 When using this tool, please cite :
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147
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148 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_
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149
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150 As CRMAv2 normalization is used, please also cite `H. Bengtsson, P. Wirapati, and T. P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics, 5(17):2149–2156, 2009. <http://bioinformatics.oxfordjournals.org/content/25/17/2149.short>`_
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151
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152 When using TumorBoost to improve normalization in a normal-tumor study, please cite `H. Bengtsson, P. Neuvial, and T. P. Speed. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics, 11, 2010 <http://www.biomedcentral.com/1471-2105/11/245>`_
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153
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154 </help>
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155 </tool>
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