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1 <tool id="extract" name="Extract" force_history_refresh="True">
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2 <description>copy number or allele B fraction signal</description>
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3 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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4 <command interpreter="python">
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5 extractCN.py
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6 --chrom '$chrom'
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7 --input '$input'
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8 --output '$output'
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9 --new_file_path '$__new_file_path__'
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10 #if $settings.settingsType == "file":
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11 --settings_type '$settings.inputs'
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12 #end if
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13 #if $settings.settingsType == "dataset":
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14 --settings_type 'dataset'
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15 #end if
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16 #if $settingsSNP.signal == "fracB":
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17 --settings_snp 'TRUE'
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18
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19 #if $settingsSNP.sym.symmetrize=="TRUE"
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20 --settings_tumor '$tumorcsvFracBsym'
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21 #elif $settingsSNP.sym.symmetrize=="FALSE"
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22 #if $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "standard":
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23 --settings_tumor 'None'
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24 #elif $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "tumor":
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25 --settings_tumor '$tumorcsvFracB'
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26 #end if
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27 #end if
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28 --symmetrize '$settingsSNP.sym.symmetrize'
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29 #else
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30 --settings_snp '$settingsSNP.snp'
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31 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
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32 --settings_tumor 'None'
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33 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
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34 --settings_tumor '$tumorcsvCN'
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35 #end if
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36 #end if
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37 --outputlog '$outputlog'
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38 --log '$log'
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39 --settings_signal '$settingsSNP.signal'
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40 --userid '$__user_id__'
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41 </command>
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42 <inputs>
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43 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
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44 <conditional name="settings">
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45 <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset">
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46 <option value="dataset">Select whole dataset</option>
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47 <option value="file">Select file individually</option>
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48 </param>
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49 <when value="dataset"/>
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50 <when value="file">
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51 <param name="inputs" type="select" format="cel" multiple="true" label="Cel files">
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52 <options from_dataset="input">
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53 <column name="name" index="0"/>
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54 <column name="value" index="0"/>
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55 </options>
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56 </param>
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57 </when>
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58 </conditional>
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59
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60 <conditional name="settingsSNP">
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61 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
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62 <option value="CN">CN</option>
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63 <option value="fracB">fracB</option>
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64 </param>
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65 <when value="fracB">
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66 <conditional name="sym">
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67 <param name="symmetrize" type="select" label="Symmetrize allele B signal">
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68 <option value="TRUE">Yes</option>
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69 <option value="FALSE">No</option>
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70 </param>
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71 <when value="TRUE">
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72 <param name="tumorcsvFracBsym" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
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73 </when>
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74 <when value="FALSE">
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75 <conditional name="settingsTumorFracB">
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76 <param name="settingsTypeTumorFracB" type="select" label="Reference">
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77 <option value="standard">Study without reference</option>
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78 <option value="tumor">Normal-tumor study</option>
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79 </param>
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80 <when value="standard"/>
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81 <when value="tumor">
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82 <param name="tumorcsvFracB" type="data" format="csv" label="Tumor boost csv file" help="Normal-tumor csv file. See below for more information."/>
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83 </when>
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84 </conditional>
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85 </when>
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86 </conditional>
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87 </when>
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88 <when value="CN">
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89 <conditional name="settingsTumor">
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90 <param name="settingsTypeTumor" type="select" label="Reference">
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91 <option value="standard">Study without reference</option>
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92 <option value="tumor">Normal-tumor study</option>
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93 </param>
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94 <when value="standard"/>
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95 <when value="tumor">
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96 <param name="tumorcsvCN" type="data" format="csv" label="Normal tumor csv file" help="Normal-tumor csv file. See below for more information."/>
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97 </when>
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98 </conditional>
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99 <param name="snp" type="select" label="Select Probes">
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100 <option value="FALSE">CN and SNP probes</option>
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101 <option value="TRUE">Only SNP probes</option>
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102 </param>
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103 </when>
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104 </conditional>
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105
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106 <!--param name="chrom" type="text" value="All" label="Chromosomes" help="Chromosomes to segment. Use comma to choose multiple chromosomes: e.g. 1, 3, 8. Use 'All' for a segmentation on all chromosomes" /-->
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107
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108 <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="You can select several chromosomeleave blank for all chromosomes">
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109 <option value="All">All</option>
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110 <option value="1">chr 1</option>
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111 <option value="2">chr 2</option>
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112 <option value="3">chr 3</option>
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113 <option value="4">chr 4</option>
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114 <option value="5">chr 5</option>
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115 <option value="6">chr 6</option>
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116 <option value="7">chr 7</option>
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117 <option value="8">chr 8</option>
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118 <option value="9">chr 9</option>
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119 <option value="10">chr 10</option>
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120 <option value="11">chr 11</option>
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121 <option value="12">chr 12</option>
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122 <option value="13">chr 13</option>
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123 <option value="14">chr 14</option>
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124 <option value="15">chr 15</option>
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125 <option value="16">chr 16</option>
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126 <option value="17">chr 17</option>
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127 <option value="18">chr 18</option>
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128 <option value="19">chr 19</option>
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129 <option value="20">chr 20</option>
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130 <option value="21">chr 21</option>
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131 <option value="22">chr 22</option>
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132 <option value="23">chr 23</option>
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133 <option value="24">chr 24</option>
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134 <option value="25">chr 25</option>
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135
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136 </param>
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137
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138 <param name="outputlog" type="select" label="Output log">
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139 <option value="TRUE">Yes</option>
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140 <option value="FALSE">No</option>
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141 </param>
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142 </inputs>
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143 <outputs>
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144 <data format="sef" name="output" label="signal extraction of ${input.name}" />
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145 <data format="log" name="log" label="log of signal extraction of ${input.name}">
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146 <filter>outputlog == "TRUE"</filter>
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147 </data>
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148 </outputs>
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149 <stdio>
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150 <exit_code range="1:" level="fatal" description="See logs for more details" />
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151 </stdio>
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152 <help>
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153 .. class:: warningmark
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154
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155 Data normalization must be run (with the data normalization tool) prior to signal extraction.
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156
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157 -----
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158
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159 **What it does**
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160 This tool extracts the copy number profile from the normalized data.
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161
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162 Outputs:
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163
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164 *A tabular text file containing 3 fixed columns and 1 column per sample:*
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165
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166 - chr: Chromosome.
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167 - position: Genomic position (in bp).
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168 - probeNames: Name of the probes of the microarray.
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169 - One column per sample which contains the copy number profile for each sample.
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170
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171 -----
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172
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173 **Normal-tumor study**
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174
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175 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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176
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177 - The first column contains the names of the files corresponding to normal samples of the dataset.
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178
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179 - The second column contains the names of the tumor samples files.
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180
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181 - Column names of these two columns are respectively normal and tumor.
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182
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183 - Columns are separated by a comma.
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184
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185 - *Extensions of the files (.CEL for example) should be removed*
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186
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187
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188
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189 **Example**
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190
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191 Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
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192
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193 patient1_normal.cel
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194 patient1_tumor.cel
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195 patient2_normal.cel
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196 patient2_tumor.cel
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197 patient3_normal.cel
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198 patient3_tumor.cel
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199
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200
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201 The csv file should look like this ::
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202
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203 normal,tumor
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204 patient1_normal,patient1_tumor
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205 patient2_normal,patient2_tumor
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206 patient3_normal,patient3_tumor
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207
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208 -----
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209
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210
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211 **Citation**
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212
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213 If you use this tool please cite :
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214
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215 `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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216
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217
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218 </help>
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219 </tool>
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