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annotate preprocess.xml @ 1:b3acec804ebc draft

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
author sblanck
date Tue, 12 May 2020 10:46:30 -0400
parents 4d539083cf7f
children 3fcbb8030fcc
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1 <tool id="preprocess" name="Data Normalization" force_history_refresh="True" version="1.1.0">
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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 <command>
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8 <![CDATA[
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9 Rscript
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10 ${__tool_directory__}/preprocess.R
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11 --summary '$summary'
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12 --new_file_path '$__new_file_path__'
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13 --inputcdffull_name '$inputcdffull.name'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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14 --inputufl_name '$inputufl.name'
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15 --inputugp_name '$inputugp.name'
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16 --inputacs_name '$inputacs.name'
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17 --inputcdffull '$inputcdffull'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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18 --inputufl '$inputufl'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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19 --inputugp '$inputugp'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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20 --inputacs '$inputacs'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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21 --dataSetName '$datasetName'
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22 #if $settings.settingsType == "tumor":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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23 --tumorcsv '$tumorcsv'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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24 #end if
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25 #if $settings.settingsType == "standard":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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26 --tumorcsv 'none'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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27 #end if
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28 --settingsType '$settings.settingsType'
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29 --outputgraph '$outputgraph'
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30 --zipfigures '$zipfigures'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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37 </command>
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38 <inputs>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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39 <param name="datasetName" type="text" label="Dataset Name"/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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)." />
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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)."/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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)."/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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)."/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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="zip" name="zipfigures" label="figures of normalization of ${datasetName}">
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76 <filter>outputgraph == "TRUE"</filter>
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77 </data>
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78 <data format="log" name="log" label="log of normalization ${datasetName}">
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79 <filter>outputlog == "TRUE"</filter>
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80 </data>
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81 </outputs>
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82
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83 <stdio>
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84 <exit_code range="1:" level="fatal" description="See logs for more details" />
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85 </stdio>
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86
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87 <help>
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88
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89 **What it does**
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90
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91 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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92 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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93
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94 -----
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95
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96 **Chip file naming conventions**
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97
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98 Chip filenames must strictly follow the following rules :
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99
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100 - *.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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101
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102 - *.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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103
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104 - *.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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105
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106 - *.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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107
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108 -----
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109
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110 **Normal-tumor study with TumorBoost**
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111
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112 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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113
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114 - The first column contains the names of the files corresponding to normal samples of the dataset.
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115
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116 - The second column contains the names of the tumor samples files.
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117
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118 - Column names of these two columns are respectively normal and tumor.
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119
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120 - Columns are separated by a comma.
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121
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122 - *Extensions of the files (.CEL for example) should be removed*
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123
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124
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125
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126 **Example**
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127
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128 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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129
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130 patient1_normal.cel
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131 patient1_tumor.cel
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132 patient2_normal.cel
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133 patient2_tumor.cel
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134 patient3_normal.cel
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135 patient3_tumor.cel
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136
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137
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138 The csv file should look like this ::
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139
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140 normal,tumor
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141 patient1_normal,patient1_tumor
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142 patient2_normal,patient2_tumor
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143 patient3_normal,patient3_tumor
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144
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145
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146 -----
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147
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148 **Citation**
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149
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150 When using this tool, please cite :
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151
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152 `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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153
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154 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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155
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156 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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157
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158 </help>
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159 </tool>