Mercurial > repos > sblanck > mpagenomics

annotate preprocess.xml @ 6:7076911e5c64 draft default tip

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"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit a644ed69951bcc1ac46426c5e6c9a0af1003a9a8-dirty"
author sblanck
date Tue, 20 Apr 2021 15:00:42 +0000
parents 4f753bb8681e
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4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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1 <tool id="preprocess" name="Data Normalization" version="1.3.0">
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2 <requirements>
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3 <container type="docker">sblanck/mpagenomicsdependencies</container>
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4 </requirements>
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5
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6 <command>
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7 <![CDATA[
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8 Rscript
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9 ${__tool_directory__}/preprocess.R
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10 --summary '$summary'
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11 --new_file_path '$zipresults.files_path'
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12 --inputcdffull_name '$inputcdffull.name'
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13 --inputufl_name '$inputufl.name'
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14 --inputugp_name '$inputugp.name'
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15 --inputacs_name '$inputacs.name'
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16 --inputcdffull '$inputcdffull'
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17 --inputufl '$inputufl'
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18 --inputugp '$inputugp'
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19 --inputacs '$inputacs'
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20 --dataSetName '$datasetName'
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21 #if $settings.settingsType == "tumor":
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22 --tumorcsv '$tumorcsv'
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23 #end if
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24 #if $settings.settingsType == "standard":
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25 --tumorcsv 'none'
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26 #end if
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27 --settingsType '$settings.settingsType'
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28 --outputgraph '$outputgraph'
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29 --zipfigures '$zipfigures'
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30 --zipresults '$zipresults'
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31 --outputlog '$outputlog'
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32 --log '$log'
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33 --user_id '$__user_id__'
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34 --input "#for $input in $inputs# $input;$input.name, #end for#"
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35 ]]>
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36
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37 </command>
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38 <inputs>
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39 <param name="datasetName" type="text" label="Dataset Name"/>
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40 <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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41 <param name="inputcdffull" type="data" format="cdf" label="cdf file" help=".cdf file name must comply with the following format : &lt; chiptype &gt;,&lt; tag &gt;.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf)." />
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42 <param name="inputufl" type="data" format="ufl" label="ufl file" help=".ufl file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl)."/>
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43 <param name="inputugp" type="data" format="ugp" label="ugp file" help=".ugp file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp)."/>
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44 <param name="inputacs" type="data" format="acs" label="acs file" help=".acs file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs)."/>
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45 <conditional name="settings">
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46 <param name="settingsType" type="select" label="Reference">
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47 <option value="standard">Study without reference</option>
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48 <option value="tumor">Normal-tumor study with TumorBoost</option>
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49 </param>
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50 <when value="standard" />
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51 <when value="tumor">
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52 <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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53 </when>
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54 </conditional>
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55 <!--param name="outputgraph" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output figures" /-->
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56 <!--param name="outputlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output log" /-->
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57 <param name="outputgraph" type="select" label="Output figures">
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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="outputlog" type="select" label="Output log">
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62 <option value="TRUE">Yes</option>
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63 <option value="FALSE">No</option>
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64 </param>
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65 <!--param name="chipType" type="text" label="chipType" /-->
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66 <!--param name="workspace" type="text" label="Workspace"/-->
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67 </inputs>
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68
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69 <outputs>
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70 <!-- Would like to make this hidden or not appear all together, but
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71 variable outputs require a primary dataset. If hidden refresh
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72 doesn't occur.
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73 -->
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74 <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
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75 <data format="nzip" name="zipresults" label="Results of normalization of ${datasetName}"/>
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76 <data format="zip" name="zipfigures" label="Figures of normalization of ${datasetName}">
0
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77 <filter>outputgraph == "TRUE"</filter>
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78 </data>
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79 <data format="log" name="log" label="log of normalization ${datasetName}">
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80 <filter>outputlog == "TRUE"</filter>
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81 </data>
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82 </outputs>
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83
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84 <stdio>
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85 <exit_code range="1:" level="fatal" description="See logs for more details" />
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86 </stdio>
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87
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88 <help>
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89
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90 **What it does**
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91
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92 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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93 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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94
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95 -----
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96
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97 **Chip file naming conventions**
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98
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99 Chip filenames must strictly follow the following rules :
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100
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101 - *.cdf* filename must comply with the following format : &lt; chiptype &gt;,&lt; tag &gt;.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf). Note the use of a comma (not a point) between &lt;chiptype&gt; and the tag "Full".
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102
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103 - *.ufl* filename must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl).
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104
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105 - *.ugp* filename must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp).
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106
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107 - *.acs* file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs).
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108
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109 -----
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110
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111 **Normal-tumor study with TumorBoost**
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112
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113 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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114
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115 - The first column contains the names of the files corresponding to normal samples of the dataset.
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116
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117 - The second column contains the names of the tumor samples files.
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118
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119 - Column names of these two columns are respectively normal and tumor.
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120
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121 - Columns are separated by a comma.
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122
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123 - *Extensions of the files (.CEL for example) should be removed*
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124
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125
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126
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127 **Example**
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128
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129 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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130
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131 patient1_normal.cel
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132 patient1_tumor.cel
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133 patient2_normal.cel
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134 patient2_tumor.cel
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135 patient3_normal.cel
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136 patient3_tumor.cel
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137
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138
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139 The csv file should look like this ::
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140
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141 normal,tumor
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142 patient1_normal,patient1_tumor
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143 patient2_normal,patient2_tumor
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144 patient3_normal,patient3_tumor
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145
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146
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147 -----
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148
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149 **Citation**
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150
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151 When using this tool, please cite :
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152
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153 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
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154
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155 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 &amp; 6. Bioinformatics, 5(17):2149–2156, 2009. &lt;http://bioinformatics.oxfordjournals.org/content/25/17/2149.short&gt;`_
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156
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157 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 &lt;http://www.biomedcentral.com/1471-2105/11/245&gt;`_
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158
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159 </help>
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160 </tool>