Mercurial > repos > fcaramia > contra
annotate contra.xml @ 24:6bcf47cc272a
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author | fcaramia |
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date | Mon, 19 May 2014 20:00:44 -0400 |
parents | 2770f49cb0dc |
children | c361b3fb806e |
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1 <tool id="contra_tool" name="Contra Copy number analysis" version="1.0.0"> |
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2 <description>: Copy Number Analysis for Targeted Resequencing</description> |
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3 <requirements> |
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4 <requirement type="package" version="2.17.0">bedtools</requirement> |
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5 <requirement type="package" name="samtools" version="0.1.18">samtools</requirement> |
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6 <requirement type="package" name="contra" version="2.0.4">contra</requirement> |
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7 </requirements> |
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8 <command interpreter="perl"> |
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9 |
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10 contra_wrapper.pl |
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11 |
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12 ##Ref Genome |
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13 #if $genomeSource.refGenomeSource == "history": |
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14 "PLAYEROPTION::-f=${genomeSource.ownFile}" |
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15 #else: |
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16 ##use precomputed indexes |
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17 "PLAYEROPTION::-f=${genomeSource.indices.fields.path}" |
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18 #end if |
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19 |
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20 ##Required files |
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21 "PLAYEROPTION::-t=$target_file" |
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22 "PLAYEROPTION::-s=$alignment_file" |
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23 #if $controlSource.refControlSource == "history": |
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24 "PLAYEROPTION::-c=${controlSource.control_file}" |
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25 #else: |
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26 ##use precomputed indexes |
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27 "PLAYEROPTION::-c=${controlSource.indices.fields.path}" |
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28 #end if |
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29 |
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30 ##Optional parameter |
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31 |
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32 #if $option.option == "modify_parameters": |
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33 |
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34 "PLAYEROPTION::--numBin=$option.numBin" |
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35 "PLAYEROPTION::--minReadDepth=$option.minReadDepth" |
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36 "PLAYEROPTION::--minNBases=$option.minNbases" |
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37 |
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38 #if str($option.sam) == "true": |
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39 "PLAYEROPTION::--sam" |
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40 #end if |
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41 |
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42 #if str($option.bed) == "true": |
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43 "PLAYEROPTION::--bed" |
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44 #end if |
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45 |
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46 "PLAYEROPTION::--pval=$option.pval" |
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47 "PLAYEROPTION::--sampleName=$option.sampleName" |
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48 |
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49 #if str($option.nomultimapped) == "true": |
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50 "PLAYEROPTION::--nomultimapped" |
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51 #end if |
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52 |
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53 #if str($option.plot) == "true": |
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54 "PLAYEROPTION::--plot" |
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55 #end if |
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56 |
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57 "PLAYEROPTION::--minExon=$option.minExon" |
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58 "PLAYEROPTION::--minControlRdForCall=$option.minControlRdForCall" |
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59 "PLAYEROPTION::--minTestRdForCall=$option.minTestRdForCall" |
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60 "PLAYEROPTION::--minAvgForCall=$option.minAvgForCall" |
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61 "PLAYEROPTION::--maxRegionSize=$option.maxRegionSize" |
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62 "PLAYEROPTION::--targetRegionSize=$option.targetRegionSize" |
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63 |
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64 #if str($option.largedeletion) == "true": |
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65 "PLAYEROPTION::--largedeletion" |
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66 #end if |
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67 |
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68 "PLAYEROPTION::--smallSegment=$option.smallSegment" |
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69 "PLAYEROPTION::--targetRegionSize=$option.targetRegionSize" |
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70 "PLAYEROPTION::--largeSegment=$option.largeSegment" |
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71 "PLAYEROPTION::--lrCallStart=$option.lrCallStart" |
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72 "PLAYEROPTION::--lrCallEnd=$option.lrCallEnd" |
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73 "PLAYEROPTION::--passSize=$option.passSize" |
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74 #end if |
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75 |
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76 ##File to generate the bam list |
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77 CONTRAOUTPUT::$html_file |
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78 CONTRADIR::$html_file.files_path |
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79 |
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80 </command> |
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81 <inputs> |
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82 |
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83 <conditional name="genomeSource"> |
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84 <param name="refGenomeSource" type="select" label="Will you select a reference from your history or use a built-in fasta file?"> |
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85 <option value="indexed">Use a built-in index</option> |
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86 <option value="history">Use one from the history</option> |
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87 </param> |
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88 <when value="indexed"> |
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89 <param name="indices" type="select" label="Select a reference genome"> |
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90 <options from_data_table="all_fasta"> |
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91 <filter type="sort_by" column="2" /> |
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92 <validator type="no_options" message="No indexes are available" /> |
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93 </options> |
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94 </param> |
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95 </when> |
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96 <when value="history"> |
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97 <param name="ownFile" type="data" format="fasta" label="Select a reference from history" /> |
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98 </when> |
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99 </conditional> |
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100 |
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101 <param name="target_file" type="data" format="bed" help="" optional="false" /> |
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102 <param name="alignment_file" type="data" format="bam,sam" help="" optional="false" /> |
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103 |
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104 |
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105 <conditional name="controlSource"> |
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106 <param name="refControlSource" type="select" label="Will you select a reference from your history or use a built-in control file?"> |
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107 <option value="indexed">Use a built-in control</option> |
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108 <option value="history">Use one from the history</option> |
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109 </param> |
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110 <when value="indexed"> |
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111 <param name="indices" type="select" label="Select a baseline control"> |
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112 <options from_data_table="baseline_files"> |
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113 <filter type="sort_by" column="2" /> |
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114 <validator type="no_options" message="No files available" /> |
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115 </options> |
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116 </param> |
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117 </when> |
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118 <when value="history"> |
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119 <param name="control_file" type="data" format="bam,sam,bed,tabular" help="" optional="false" /> |
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120 </when> |
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121 </conditional> |
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122 |
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123 <conditional name="option"> |
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124 <param name="option" type="select" label="Optional Parameters" help="" optional="true"> |
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125 <option value="default_parameters" selected="true">Default Parameters</option> |
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126 <option value="modify_parameters">Modify Parameters</option> |
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127 </param> |
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128 <when value="modify_parameters"> |
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129 <param name="numBin" type="integer" value="20" optional="true" /> |
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130 <param name="minReadDepth" type="integer" value="10" optional="true" /> |
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131 <param name="minNbases" type="integer" value="10" optional="true" /> |
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132 <param name="sam" type="select" label="sam" help="" optional="true"> |
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133 <option value="true" >true</option> |
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134 <option value="false" selected="true">false</option> |
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135 </param> |
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136 <param name="bed" type="select" label="bed" help="" optional="true"> |
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137 <option value="true" >true</option> |
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138 <option value="false" selected="true">false</option> |
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139 </param> |
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140 <param name="pval" type="float" value="0.05" optional="true" /> |
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141 <param name="sampleName" value="Contra_Output" type="text" optional="true" /> |
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142 <param name="nomultimapped" type="select" label="no multimapped" help="" optional="true"> |
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143 <option value="true" >true</option> |
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144 <option value="false" selected="true">false</option> |
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145 </param> |
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146 <param name="plot" type="select" label="plot" help="" optional="true"> |
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147 <option value="true" >true</option> |
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148 <option value="false" selected="true">false</option> |
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149 </param> |
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150 <param name="minExon" type="integer" value="2000" optional="true" /> |
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151 <param name="minControlRdForCall" type="integer" value="5" optional="true" /> |
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152 <param name="minTestRdForCall" type="integer" value="0" optional="true" /> |
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153 <param name="minAvgForCall" type="integer" value="20" optional="true" /> |
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154 <param name="maxRegionSize" type="integer" value="0" optional="true" /> |
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155 <param name="targetRegionSize" type="integer" value="200" optional="true" /> |
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156 <param name="largedeletion" type="select" label="large deletion" help="" optional="true"> |
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157 <option value="true" >true</option> |
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158 <option value="false" selected="true">false</option> |
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159 </param> |
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160 |
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161 <param name="smallSegment" type="integer" value="1" optional="true" /> |
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162 <param name="largeSegment" type="integer" value="25" optional="true" /> |
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163 <param name="lrCallStart" type="float" value="-0.3" optional="true" /> |
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164 <param name="lrCallEnd" type="float" value="0.3" optional="true" /> |
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165 <param name="passSize" type="float" value="0.5" optional="true" /> |
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166 |
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167 </when> |
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168 </conditional> |
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169 </inputs> |
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170 <outputs> |
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171 <data name="html_file" format="html" label="Contra Output" /> |
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172 </outputs> |
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173 <help> |
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174 | |
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175 |
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176 |
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177 **Reference** |
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178 http://contra-cnv.sourceforge.net/ |
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179 |
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180 ----- |
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181 |
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182 **What it does** |
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183 |
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184 CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package. |
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185 |
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186 |
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187 ----- |
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188 |
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189 **Required Parameters** |
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190 |
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191 :: |
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192 |
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193 -t, --target Target region definition file [BED format] |
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194 |
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195 -s, --test Alignment file for the test sample [BAM/SAM] |
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196 |
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197 -c, --control Alignment file for the control sample |
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198 [BAM/SAM/BED – baseline file] |
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199 |
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200 --bed **option has to be supplied for control |
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201 with baseline file.** |
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202 |
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203 -f, --fasta Reference genome [FASTA] |
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204 |
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205 -o, --outFolder the folder name (and its path) to store the output |
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206 of the analysis (this new folder will be created – |
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207 error message occur if the folder exists) |
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208 |
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209 ----- |
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210 |
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211 **Optional Parameters** |
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212 |
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213 :: |
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214 |
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215 --numBin Numbers of bins to group the regions. User can |
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216 specify multiple experiments with different numbers |
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217 of bins (comma separated). [Default: 20] |
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218 |
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219 --minReadDepth The threshold for minimum read depth for each bases |
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220 (see Step 2 in CONTRA workflow) [Default: 10] |
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221 |
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222 --minNBases The threshold for minimum number of bases for each |
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223 target regions (see Step 2 in CONTRA workflow) |
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224 [Default: 10] |
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225 |
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226 --sam If the specified test and control samples are in |
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227 SAM format. [Default: False] (It will always take |
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228 BAM samples as default) |
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229 |
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230 --bed If specified, control will be a baseline file in |
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231 BED format. [Default: False] |
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232 Please refer to the Baseline Script section for |
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233 instruction how to create baseline files from set |
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234 of BAMfiles. A set of baseline files from different |
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235 platform have also been provided in the CONTRA |
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236 download page. |
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237 |
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238 --pval The p-value threshold for filtering. Based on Adjusted |
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239 P-Values. Only regions that pass this threshold will |
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240 be included in the VCF file. [Default: 0.05] |
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241 |
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242 --sampleName The name to be appended to the front of the default output |
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243 name. By default, there will be nothing appended. |
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244 |
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245 --nomultimapped The option to remove multi-mapped reads |
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246 (using SAMtools with mapping quality > 0). |
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247 [default: FALSE] |
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248 |
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249 -p, --plot If specified, plots of log-ratio distribution for each |
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250 bin will be included in the output folder [default: FALSE] |
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251 |
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252 --minExon Minimum number of exons in one bin (if less than this number |
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253 , bin that contains small number of exons will be merged to |
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254 the adjacent bins) [Default : 2000] |
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255 |
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256 --minControlRdForCall Minimum Control ReadDepth for call [Default: 5] |
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257 |
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258 --minTestRdForCall Minimum Test ReadDepth for call [Default: 0] |
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259 |
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260 --minAvgForCall Minimum average coverage for call [Default: 20] |
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261 |
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262 --maxRegionSize Maximum region size in target region (for breaking |
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263 large regions into smaller regions. By default, |
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264 maxRegionSize=0 means no breakdown). [Default : 0] |
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265 |
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266 --targetRegionSize Target region size for breakdown (if maxRegionSize |
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267 is non-zero) [Default: 200] |
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268 |
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269 -l, --largeDeletion If specified, CONTRA will run large deletion analysis (CBS). |
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270 User must have DNAcopy R-library installed to run the |
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271 analysis. [False] |
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272 |
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273 --smallSegment CBS segment size for calling large variations [Default : 1] |
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274 |
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275 --largeSegment CBS segment size for calling large variations [Default : 25] |
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276 |
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277 --lrCallStart Log ratios start range that will be used to call CNV |
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278 [Default : -0.3] |
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279 |
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280 --lrCallEnd Log ratios end range that will be used to call CNV |
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281 [Default : 0.3] |
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282 |
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283 --passSize Size of exons that passed the p-value threshold compare |
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284 to the original exons size [Default: 0.5] |
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285 </help> |
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286 </tool> |
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287 |
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288 |