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1 <tool id="preprocess2" name="Data Normalization" force_history_refresh="True" version="0.1.0">
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3 <command interpreter="python">
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4 preprocess2.py
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5 -s '$summary'
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6 -p '$__new_file_path__'
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7 -c '$inputcdffull.name'
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8 -f '$inputufl.name'
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9 -g '$inputugp.name'
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10 -a '$inputacs.name'
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11 -d '$inputcdffull'
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12 -v '$inputufl'
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13 -w '$inputugp'
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14 -b '$inputacs'
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15 -e 'datasetName'
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16 #if $settings.settingsType == "tumor":
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17 -t '$tumorcsv'
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18 #end if
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19 #if $settings.settingsType == "standard":
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20 -t 'none'
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21 #end if
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22 -y '$settings.settingsType'
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23 -o '$outputgraph'
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24 -z '$zipfigures'
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25 -k '$outputlog'
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26 -l '$log'
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27 -u '$__user_id__'
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28 #for $input in $inputs
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29 -i "${input}"
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30 -n "${input.name}"
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31 #end for
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32 </command>
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33 <inputs>
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34 <param name="datasetName" type="text" label="Dataset Name"/>
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35 <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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36 <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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37 <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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38 <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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39 <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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40 <conditional name="settings">
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41 <param name="settingsType" type="select" label="Reference">
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42 <option value="standard">Study without reference</option>
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43 <option value="tumor">Normal-tumor study with TumorBoost</option>
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44 </param>
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45 <when value="standard" />
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46 <when value="tumor">
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47 <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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48 </when>
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49 </conditional>
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50 <!--param name="outputgraph" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output figures" /-->
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51 <!--param name="outputlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output log" /-->
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52 <param name="outputgraph" type="select" label="Output figures">
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53 <option value="TRUE">Yes</option>
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54 <option value="FALSE">No</option>
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55 </param>
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56 <param name="outputlog" type="select" label="Output log">
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57 <option value="TRUE">Yes</option>
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58 <option value="FALSE">No</option>
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59 </param>
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60 <!--param name="chipType" type="text" label="chipType" /-->
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61 <!--param name="workspace" type="text" label="Workspace"/-->
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62 </inputs>
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63
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64 <outputs>
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65 <!-- Would like to make this hidden or not appear all together, but
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66 variable outputs require a primary dataset. If hidden refresh
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67 doesn't occur.
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68 -->
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69 <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
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70 <data format="zip" name="zipfigures" label="figures of normalization of ${datasetName}">
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71 <filter>outputgraph == "TRUE"</filter>
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72 </data>
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73 <data format="log" name="log" label="log of normalization ${datasetName}">
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74 <filter>outputlog == "TRUE"</filter>
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75 </data>
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76 </outputs>
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77
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78 <stdio>
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79 <exit_code range="1:" level="fatal" description="See logs for more details" />
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80 </stdio>
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81
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82 <help>
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83
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84 **What it does**
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85
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86 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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87 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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88
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89 -----
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90
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91 **Chip file naming conventions**
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92
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93 Chip filenames must strictly follow the following rules :
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94
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95 - *.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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96
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97 - *.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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98
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99 - *.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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100
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101 - *.acs* file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs).
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102
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103 -----
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104
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105 **Normal-tumor study with TumorBoost**
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106
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107 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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108
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109 - The first column contains the names of the files corresponding to normal samples of the dataset.
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110
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111 - The second column contains the names of the tumor samples files.
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112
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113 - Column names of these two columns are respectively normal and tumor.
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114
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115 - Columns are separated by a comma.
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116
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117 - *Extensions of the files (.CEL for example) should be removed*
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118
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119
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120
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121 **Example**
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122
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123 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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124
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125 patient1_normal.cel
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126 patient1_tumor.cel
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127 patient2_normal.cel
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128 patient2_tumor.cel
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129 patient3_normal.cel
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130 patient3_tumor.cel
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131
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132
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133 The csv file should look like this ::
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134
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135 normal,tumor
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136 patient1_normal,patient1_tumor
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137 patient2_normal,patient2_tumor
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138 patient3_normal,patient3_tumor
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139
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140
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141 -----
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142
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143 **Citation**
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144
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145 When using this tool, please cite :
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146
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147 `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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148
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149 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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150
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151 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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152
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153 </help>
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154 </tool>
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