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1 <tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
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18
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2 <description>Smooth and Plot</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <stdio>
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8 <exit_code range="255" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
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9 <exit_code range="10" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
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10 <exit_code range="11" level="fatal" description="Not all region files are present in the first column of header file for regions." />
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11 <exit_code range="20" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
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12 <exit_code range="21" level="fatal" description="Not all feature files are present in the first column of header file for features." />
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13 <exit_code range="30" level="fatal" description="An error has occurred reading the data. Please try again." />
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14 <exit_code range="31" level="fatal" description="Not enough columns in input file." />
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15 <exit_code range="32" level="fatal" description="Duplicated regions in region file." />
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16 <exit_code range="33" level="fatal" description="Duplicated windows in feature file." />
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17 <exit_code range="34" level="fatal" description="Overlapping windows in feature file." />
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18 <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." />
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19 <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." />
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20 <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." />
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21 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
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22 </stdio>
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23
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24 <command>
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25 <![CDATA[
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26 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
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27
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28 #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
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29 regionspaths='${region_paths}'
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30 #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
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31 regionsgalaxyids='c(${region_galaxyids})'
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32 #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
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33 regionsfilenames='${region_names}'
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34 #set region_header = $regionsheadersection.regionsheader
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35 #if $region_header != "":
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36 regionsheaderfile='${region_header}'
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37 #end if
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38
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39 #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
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40 featurespaths='${feature_paths}'
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41 #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
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42 featuresgalaxyids='c(${feature_galaxyids})'
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43 #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
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44 featuresfilenames='${feature_names}'
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45 #set feature_header = $featuresheadersection.featuresheader
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46 #if $feature_header != "":
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47 featuresheaderfile='${feature_header}'
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48 #end if
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49
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50 smoothing="'${conditionaltype.smoothing}'"
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51 start.are.0based='${zerobased}'
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52 #if $conditionaltype.smoothing == 'no':
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53 alignment="'${conditionaltype.alignment}'"
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54 #elif $conditionaltype.smoothing == 'locpoly':
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55 alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
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56 #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
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57 scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
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58 #end if
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59 bandwidth='${conditionaltype.locpolybandwidth}'
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60 degree='${conditionaltype.locpolydegree}'
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61 fill_gaps='${conditionaltype.fillgaps}'
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62 #elif $conditionaltype.smoothing == 'kernel':
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63 alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
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64 #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
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65 scale='${conditionaltype.kernelconditionalscale.scalegrid}'
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66 #end if
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67 bandwidth='${conditionaltype.kernelbandwidth}'
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68 fill_gaps='${conditionaltype.fillgaps}'
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69 #elif $conditionaltype.smoothing == 'splines':
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70 alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
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71 #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
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72 scale='${conditionaltype.splinesconditionalscale.scalegrid}'
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73 #end if
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74 degree='${conditionaltype.splinesdegree}'
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75 dist_knots='${conditionaltype.splinesdistknots}'
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76 fill_gaps='${conditionaltype.fillgaps}'
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77 #end if
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78
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79 average='${plotres.average}'
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80 size='${plotres.size}'
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81 plottype="'${plotres.conditionalplottype.plottype}'"
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82 #if $plotres.conditionalplottype.plottype == 'boxplot':
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83 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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84 #if $probs != "":
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85 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
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86 #else:
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87 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
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88 #end if
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89 #end if
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90
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91 >& /dev/null
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92 ]]>
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93 <!--
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94 to print the stack add the following line at the end of the command and enable the corresponding entry in output
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95 2> "${stackerr}"
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96 -->
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97 </command>
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98
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99 <inputs>
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100 <!-- regions -->
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101 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
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102 <section name="regionsheadersection" title="Insert header file for regions (optional)" expanded="false" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
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103 <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" />
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104 </section>
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105
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106 <!-- features -->
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107 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
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108 <section name="featuresheadersection" title="Insert header file for features (optional)" expanded="false" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
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109 <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" />
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110 </section>
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111
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112 <!-- zero-base one-base -->
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113 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
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114 <option value="TRUE">0-based</option>
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115 <option value="FALSE">1-based</option>
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116 </param>
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117
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118 <!-- conditional smoothing -->
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119 <conditional name="conditionaltype">
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120 <!-- smoothing -->
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121 <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
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122 <option value="no">No</option>
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123 <option value="locpoly">Local Polynomials</option>
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124 <option value="kernel">Gaussian Kernel</option>
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125 <option value="splines">B-Splines</option>
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126 </param>
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127 <!-- conditional choice: smoothing=no -->
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128 <when value="no">
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129 <param name="alignment" type="select" label="Region alignment" help="">
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130 <option value="center">Center - Alignment on the central position</option>
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131 <option value="left">Left - Alignment on the starting position</option>
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132 <option value="right">Right - Alignment on the ending position</option>
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133 </param>
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134 </when>
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135 <!-- conditional choice: smoothing=locpoly -->
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136 <when value="locpoly">
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137 <!-- conditional region alignment -->
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138 <conditional name="locpolyconditionalscale">
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139 <param name="alignment" type="select" label="Region alignment" help="">
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140 <option value="center">Center - Alignment on the central position</option>
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141 <option value="left">Left - Alignment on the starting position</option>
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142 <option value="right">Right - Alignment on the ending position</option>
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143 <option value="scale">Scale - Scaling all regions to the same length</option>
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144 </param>
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145 <when value="scale">
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146 <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
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147 </when>
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148 </conditional>
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149
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150 <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
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151 <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
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152
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153 <!-- fill gaps -->
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154 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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155 </when>
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156 <!-- conditional choice: smoothing=kernel -->
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157 <when value="kernel">
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158 <!-- conditional region alignment -->
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159 <conditional name="kernelconditionalscale">
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160 <param name="alignment" type="select" label="Region alignment" help="">
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161 <option value="center">Center - Alignment on the central position</option>
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162 <option value="left">Left - Alignment on the starting position</option>
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163 <option value="right">Right - Alignment on the ending position</option>
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164 <option value="scale">Scale - Scaling all regions to the same length</option>
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165 </param>
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166 <when value="scale">
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167 <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
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168 </when>
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169 </conditional>
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170
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171 <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
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172
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173 <!-- fill gaps -->
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174 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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175 </when>
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176 <!-- conditional choice: smoothing=splines -->
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177 <when value="splines">
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178 <!-- conditional region alignment -->
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179 <conditional name="splinesconditionalscale">
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180 <param name="alignment" type="select" label="Region alignment" help="">
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181 <option value="center">Center - Alignment on the central position</option>
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182 <option value="left">Left - Alignment on the starting position</option>
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183 <option value="right">Right - Alignment on the ending position</option>
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184 <option value="scale">Scale - Scaling all regions to the same length</option>
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185 </param>
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186 <when value="scale">
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187 <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
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188 </when>
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189 </conditional>
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190
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191 <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
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192 <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
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193
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194 <!-- fill gaps -->
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195 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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196 </when>
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197 </conditional>
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198
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199 <!-- plot IWTomics results -->
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200 <section name="plotres" title="Plot data" expanded="True">
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201 <!-- average -->
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202 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
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203 <!-- sample size in each position -->
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204 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
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205 <!-- conditional plot type -->
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206 <conditional name="conditionalplottype">
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207 <!-- plot type -->
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208 <param name="plottype" type="select" label="Plot type" help="">
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209 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
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210 <option value="curves">Curves (aligned)</option>
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211 </param>
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212 <!-- conditional choice: plottype=boxplot -->
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213 <when value="boxplot">
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214 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
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215 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
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216 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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217 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
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218 <repeat name="probabilities" title="Probabilities">
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219 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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220 </repeat>
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221 </section>
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222 </when>
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223 </conditional>
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224 </section>
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225 </inputs>
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226
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227 <outputs>
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228 <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
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229 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
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230 <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
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231 <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
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232 <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
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233 </outputs>
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234
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235 <tests>
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236 <test>
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237 <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" />
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238 <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" />
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239 <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" />
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240 <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" />
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241 <param name="zerobased" value="TRUE" />
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242 <param name="smoothing" value="kernel" />
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243 <param name="alignment" value="center" />
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244 <param name="kernelbandwidth" value="5" />
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245 <param name="fillgaps" value="TRUE" />
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246 <param name="average" value="TRUE" />
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247 <param name="size" value="TRUE" />
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248 <param name="plottype" value="boxplot" />
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249 <param name="prob0" value="0.25" />
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250 <param name="prob1" value="0.5" />
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251 <param name="prob2" value="0.75" />
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252 <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" />
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253 <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" />
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254 <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" />
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255 <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" />
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256 </test>
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257 </tests>
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258
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68
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259 <help><![CDATA[
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260 This tool imports a collection of genomic region datasets, and associates to each region
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261 multiple genomic feature measurements. It allows to align the regions in multiple ways
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262 (center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
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263 measurements) and to create a graphical representation of the feature measurements in each
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264 region datasets (aligned curves or pointwise quantile curves).
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265
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266 -----
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267
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268 **Region datasets**
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269
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270 Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
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271 start end (extra columns present in the input file are ignored). Regions can be of different
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272 length::
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273
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274 chr2 49960150 50060150
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275 chr2 55912445 56012445
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276 ...
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277
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278 -----
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279
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280 **Feature measurements**
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281
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282 Feature measurements corresponding to all the regions can be provided as a BED or Tabular
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283 file with tab delimited columns chr start end value::
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284
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285 chr2 49960150 49962150 0.9426
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286 chr2 49962150 49964150 0.7816
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287 ...
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288
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289 Each feature must be measured in windows of a fixed size inside all the regions (missing
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290 values must be indicated as NA). Another way to import feature measurements is from a
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291 Tabular file with the first three columns chr start end corresponding to the different genomic
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292 regions, followed on the same row by all the measurements in fixed-size windows::
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293
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294 chr2 49960150 50060150 0.9426 0.7816 0.8921 ... ... 1.2063
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295 chr2 55912445 56012445 0.8719 0.9975 1.1619 ... ... 0.9601
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296 ...
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297
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298 -----
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299
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300 **Output**
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301
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302 The tool returns:
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303
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304 1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
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305 2. Region dataset identifiers;
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306 3. Feature identifiers;
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307 4. PDF file with the plotted data.
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308
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309 1-3 can be used as input of the tool *IWTomics Test and Plot*
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310
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311 -----
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312
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313 .. class:: infomark
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314
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315 **Notes**
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316
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317 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
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318
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319 It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
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320 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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321
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322 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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323
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324 Example data can be found at:
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325
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326 1. Simulated_data_
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327 2. ETn_data_
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328
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329 .. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
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330 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
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331 ]]></help>
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332
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333 <expand macro="citations" />
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334
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335 </tool>
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