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1 <tool id="QDNAseq" name="QDNAseq" version="0.0.1">
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2
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3 <requirements>
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4 <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> -->
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5 <!-- The R package for v3.1.0 is not ready yet -->
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6 <!--<requirement type="package" version="3.1.0">R</requirement>-->
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7 <!-- <requirement type="package" version="1.0.5">bioc_qdnaseq</requirement> -->
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8 </requirements>
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9
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10 <description>Quantitative copy number abberation detection</description>
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11
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12 <!--
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13 if case you want to use a specific R installation use the commented command block and set correct path
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14 <command>
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15 /ccagc/lib/R/R-3.1.0/bin/Rscript QDNAseq.R
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16 $qdnaseq_cfg
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17 </command>
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18 -->
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19
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20 <command interpreter="Rscript">
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21 QDNAseq.R
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22 $qdnaseq_cfg <!-- use a tmp config file to pass all params to R by source() -->
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23 </command>
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24
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25 <stdio>
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26 <!-- Anything higher than 0 means the R script didnt finish -->
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27 <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
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28 <exit_code range="1:" level="fatal" description="R script didnt finish correctly, check log" />
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29 </stdio>
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30
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31 <inputs>
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32 <!-- ==================== -->
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33 <!-- General inputs -->
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34 <!-- ==================== -->
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35 <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
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36 <validator type="empty_field" />
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37 <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
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38 </param>
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39 <param name="binSize" type="select" label="Select bin-size to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
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40 <option value="1000">1Mb</option>
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41 <option value="100">100kb</option>
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42 <option value="30">30kb</option>
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43 <option value="15">15kb</option>
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44 <option value="5">5kb</option>
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45 <option value="1">1kb</option>
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46 </param>
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47 <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
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48 <option value="TRUE">yes</option>
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49 <option value="FALSE">no</option>
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50 </param>
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51 <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
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52 <option value="SR50">Single Read 50bp</option>
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53 <!-- <option value="PE1000">PairedEnd1000</option> -->
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54 </param>
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55
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56 <!-- ==================== -->
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57 <!-- Input BAMs -->
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58 <!-- ==================== -->
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59 <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select all BAM files to include in the analysis" />
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60
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61 <!-- ==================== -->
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62 <!-- This section contains galaxy history output settings -->
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63 <!-- ==================== -->
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64 <conditional name="extra_history_outputs">
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65 <param name="show" type="select" label="Show additional history outputs">
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66 <option value="NO">Only output Report to history</option>
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67 <option value="YES">Select additional history outputs</option>
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68 </param>
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69 <when value="YES">
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70 <param name="readcounts_rds" type="select" label="Also output readcounts RDS (R object) to history">
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71 <option value="FALSE">no</option>
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72 <option value="TRUE">yes</option>
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73 </param>
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74 <param name="copynumbers_rds" type="select" label="Also output copynumbers RDS (R object) to history">
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75 <option value="FALSE">no</option>
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76 <option value="TRUE">yes</option>
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77 </param>
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78 <param name="calls_rds" type="select" label="Also output called segments RDS (R object) to history">
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79 <option value="FALSE">no</option>
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80 <option value="TRUE">yes</option>
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81 </param>
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82 </when>
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83 <when value="NO">
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84 <param name="readcounts_rds" type="hidden" value="FALSE" />
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85 <param name="copynumbers_rds" type="hidden" value="FALSE" />
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86 <param name="calls_rds" type="hidden" value="FALSE" />
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87 </when>
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88 </conditional>
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89
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90 <!-- ==================== -->
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91 <!-- Option to use your own bin annotations -->
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92 <!-- ==================== -->
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93 <conditional name="use_own_binannotation">
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94 <param name="show" type="select" label="Use your own bin annotations from history">
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95 <option value="no">no</option>
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96 <option value="yes">yes</option>
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97 </param>
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98 <when value="yes">
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99 <param name="binannotation_file" type="data" multiple="false" format="rds" label="R data structure file with bin-annotations" help="If you made your own bin-annotations with the QDNAseq bioconductor package you can upload them to your history and select here" />
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100 </when>
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101 <when value="no">
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102 <param name="binannotation_file" type="hidden" value="" />
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103 </when>
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104 </conditional>
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105 <!-- ==================== -->
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106 <!-- Optional advanced options -->
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107 <!-- ==================== -->
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108 <conditional name="advanced">
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109 <param name="show" type="select" label="Show advanced options">
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110 <option value="no">no</option>
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111 <option value="yes">yes</option>
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112 </param>
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113 <when value="yes">
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114
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115 <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
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116 <option value="sdundo">sdundo</option>
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117 <option value="prune">prune</option>
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118 <option value="none">none</option>
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119 </param>
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120
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121 <param name="undoSD" size="10" type="float" value="1" label="undoSD" help='The number of SDs between means to keep a split if undo.splits="sdundo".' />
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122
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123 <param name="blacklist" type="select" label="Filter blacklisted bins (blacklist)" help="Will exclude all blacklisted bins in the binannotation if set">
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124 <option value="TRUE">yes</option>
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125 <option value="FALSE">no</option>
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126 </param>
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127
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128 <param name="mappability" type="integer" value="0" min="0" max="100" label="Filter bins with lower mappability" help="Will exclude all bins will lower mappability than this number (0-100)" />
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129
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130 <param name="debug" type="select" label="DEBUG/TEST" help="Use inbuilt LGG data instead of input BAMs">
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131 <option value="FALSE">no</option>
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132 <option value="TRUE">yes</option>
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133 </param>
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134 </when>
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135 <!-- need to set defaults because params are passed to R anyway -->
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136 <when value="no">
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137 <param name="undoSD" type="hidden" value="1" />
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138 <param name="undo_splits" type="hidden" value="sdundo" />
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139 <param name="blacklist" type="hidden" value="TRUE" />
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140 <param name="mappability" type="hidden" value="0" />
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141 <param name="debug" type="hidden" value="FALSE" />
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142 </when>
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143 </conditional>
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144
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145 <!-- ==================== -->
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146 <!-- Optional graphical/plotting options -->
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147 <!-- ==================== -->
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148 <conditional name="plot_options">
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149 <param name="show" type="select" label="Show graphical options">
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150 <option value="no">no</option>
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151 <option value="yes">yes</option>
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152 </param>
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153 <when value="yes">
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154 <param name="plot_width" size="3" type="integer" value="960" label="Plot width" />
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155 <param name="plot_height" size="3" type="integer" value="480" label="Plot height" />
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156 <param name="exclude_chrs" type="select" multiple="true" label="Hide these chromosomes in plots" help="Currently only standard human chromosomes supported. NOTE: other filters might also exclude chromosomes">
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157 <option value="1">1</option>
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158 <option value="2">2</option>
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159 <option value="3">3</option>
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160 <option value="4">4</option>
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161 <option value="5">5</option>
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162 <option value="6">6</option>
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163 <option value="7">7</option>
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164 <option value="8">8</option>
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165 <option value="9">9</option>
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166 <option value="10">10</option>
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167 <option value="11">11</option>
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168 <option value="12">12</option>
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169 <option value="13">13</option>
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170 <option value="14">14</option>
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171 <option value="15">15</option>
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172 <option value="16">16</option>
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173 <option value="17">17</option>
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174 <option value="18">18</option>
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175 <option value="19">19</option>
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176 <option value="20">20</option>
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177 <option value="21">21</option>
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178 <option value="22">22</option>
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179 <option value="X" selected="true">X</option>
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180 <option value="Y" selected="true">Y</option>
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181 </param>
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182 </when>
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183 <when value="no">
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184 <param name="plot_width" type="hidden" value="960" />
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185 <param name="plot_height" type="hidden" value="480" />
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186 <param name="exclude_chrs" type="hidden" value="X,Y" />
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187 </when>
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188 </conditional>
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189 </inputs>
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190 <!-- ==================== -->
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191 <!-- This config is sourced in R code -->
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192 <!-- ==================== -->
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193 <configfiles>
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194 <configfile name="qdnaseq_cfg">
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195 ## this file was sourced in QDNAseq R wrapper script
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196 ## in this way all galaxy params are passes to R
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197
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198 ## required params
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199 as.integer( "${binSize}" ) -> binSize
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200 "${experimentType}" -> experimentType
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201 "${jobName}" -> outputName
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202
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203 ## extra params
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204 as.logical( "${doCall}" ) -> doCall
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205 "${htmlFile}" -> outputHtml
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206 "${htmlFile.files_path}" -> outputPath
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207 "${use_own_binannotation.binannotation_file}" -> binAnnotations
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208
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209 ## advanced options
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210 as.double( "${advanced.undoSD}" ) -> undoSD
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211 as.logical( "${advanced.debug}" ) -> debug
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212 as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
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213 as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
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214 "${advanced.undo_splits}" -> undoSplits
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215
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216 ## history output params
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217 as.logical( "${extra_history_outputs.readcounts_rds}" ) -> doOutputReadcountsRds
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218 as.logical( "${extra_history_outputs.copynumbers_rds}" ) -> doOutputCopynumbersRds
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219 as.logical( "${extra_history_outputs.calls_rds}" ) -> doOutputCallsRds
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220 "${rdsReadCounts}" -> readCountsDatasetFile
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221 "${rdsCopyNumbers}" -> copyNumbersDatasetFile
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222 "${rdsCalls}" -> calledSegmentsDatasetFile
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223
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224 ## plotting params
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225 as.integer( "${plot_options.plot_width}" ) -> PLOT_WIDTH
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226 as.integer( "${plot_options.plot_height}" ) -> PLOT_HEIGHT
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227 "${plot_options.exclude_chrs}" -> excludeChrsString
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228
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229 ## input BAMs init
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230 c() -> bamsPaths
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231 c() -> bamsNames
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232
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233 #for bam in $bams#
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234 c( bamsPaths, "${bam}" ) -> bamsPaths
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235 c( bamsNames, "${bam.name}" ) -> bamsNames
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236 #end for
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237
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238 </configfile>
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239 </configfiles>
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240
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241 <!-- ==================== -->
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242 <!-- Main output is an html based report, additional on request -->
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243 <!-- ==================== -->
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244 <outputs>
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245
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246 <data format="html" name="htmlFile" label="QDNAseq Report ${binSize}kb (${jobName})" />
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247
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248 <data format="rds" name="rdsReadCounts" label="${jobName}_readCounts_${binSize}kb.rds">
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249 <filter> extra_history_outputs['readcounts_rds'] == "TRUE" </filter><!-- <filter>("readcounts_rds" in outputs)</filter> -->
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250 </data>
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251
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252 <data format="rds" name="rdsCopyNumbers" label="${jobName}_copyNumbers_${binSize}kb.rds">
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253 <filter> extra_history_outputs['copynumbers_rds'] == "TRUE" </filter>
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254 </data>
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255
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256 <data format="rds" name="rdsCalls" label="${jobName}_calls_${binSize}kb.rds">
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257 <filter> extra_history_outputs['calls_rds'] == "TRUE" </filter>
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258 </data>
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259
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260 </outputs>
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261
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262 <!-- ==================== -->
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263 <!-- Tests still to be done -->
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264 <!-- ==================== -->
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265
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266 <!--
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267 <tests>
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268 <test>
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269 <param name="input1" value="input1" />
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270 <param name="input2" value="input2" />
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271 </test>
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272 </tests>
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273 -->
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274
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275 <help>
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276 .. class:: infomark
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277
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278 **Introduction**
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279
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280 This tool is a wrapper for the R Bioconductor package QDNAseq_
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281
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282 .. _QDNAseq: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
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283
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284 It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.
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285
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286 -----
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287
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288 .. class:: warningmark
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289
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290 As there is no R 3.1.0 package yet which is required, the **dependencies** need to be installed by hand and available to the galaxy user: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5)
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291
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292 .. class:: warningmark
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293
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294 The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.
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295
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296 .. class:: warningmark
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297
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298 Requires **internet access** for downloading bin-annotations from bitbucket and to show some styling (css) of the final report
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299
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300 -----
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301
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302 **Citation**
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303
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304 For the underlying tool please cite: llari Scheinin, Daoud Sie et al. DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions, (submitted). See also the bioconductor package_ documentation.
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305
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306 .. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
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307
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308
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309 .. image:: no_image.png
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310 </help>
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311
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312 </tool>
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