Mercurial > repos > davidvanzessen > argalaxy_tools

annotate report_clonality/circos/parse-table.conf @ 58:4c6df851e262 draft default tip

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"planemo upload commit 1a7731bb4fe2e80fb1fdc88121783068af3edb08"
author rhpvorderman
date Fri, 21 Apr 2023 10:04:39 +0000
parents 81b3eb11ed2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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2 ################################################################
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3 #
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4 # This is a fairly complicated configuration file. Take your time in
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5 # experimenting and adjust one thing at a time :)
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6 #
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7 ################################################################
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8
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9 max_col_num = 200
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10 max_row_num = 200
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11
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12 # skip this many rows before reading in header and data
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13 skip_rows = 0
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14
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15 # is there a header line that identifies the columns?
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16 header = yes
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17
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18 # is there a row that specifies the order of columns in the image?
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19 # - if so, this must be the first line of the header
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20 # - if the line exists (col_order_row=yes), employ the use_col_order_row to toggle whether it is used
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21 col_order_row = no
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22 use_col_order_row = no
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23
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24 # is there a row that specifies the size of columns in the image?
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25 # - if so, this must be the next line of the header
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26 # - if the line exists (col_size_row=yes), employ the use_col_size_row to toggle whether it is used
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27 col_size_row = no
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28 use_col_size_row = no
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29
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30 # is there a row that specifies the color of each column segment in the image?
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31 # - if so, this must be the next line of the header
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32 # - if the line exists (col_color_row=yes), employ the use_col_color_row to toggle whether it is used
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33 col_color_row = no
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34 use_col_color_row = no
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35
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36 # is there a column that specifies the order of rows in the image?
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37 # - if so, this must be the first column
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38 # - if the line exists (row_order_col=yes), employ the use_row_order_col to toggle whether it is used
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39 row_order_col = no
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40 use_row_order_col = no
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41
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42 # is there a column that specifies the color of each row segment in the image?
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43 # - if so, this must be the second column
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44 # - if the line exists (row_color_col=yes), employ the use_row_color_col to toggle whether it is used
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45 row_color_col = no
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46 use_row_color_col = no
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47
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48 # if you do not have a column/row that explicitly defines order
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49 # of segments in the image, you can set this here. Use one (or more) of
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50 # these values to specify how segments should be ordered.
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51 # - row_major (row segments first, then column)
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52 # - col_major (col segments first, then row)
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53 # - ascii (asciibetic order)
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54 # - row_size (total of rows for the segment - useful if the segment has both row and column contributions)
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55 # - col_size (total of colums for the segment - useful if the segment has both row and column contributions)
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56 # - row_to_col_ratio (ratio of total of rows to columns for the segment)
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57 # - col_to_row_ratio (ratio of total of rows to columns for the segment)
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58 # - size_asc (size, in ascending order)
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59 # - size_desc (size, in descending order)
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60
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61 #segment_order = row_to_col_ratio,size_desc # col_major,size_desc
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62 #segment_order = size_desc
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63 segment_order = row_major,size_desc
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64 #segment_order = ascii
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65 #segment_order = file:etc/order-by-table-remapped.txt
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66 #segment_order = size_desc,row_to_col_ratio
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67 segment_color_order = row_major,size_desc
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68
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69 # values for segments can be normalized if the use_segment_normalization is set to yes
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70 use_segment_normalization = no
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71
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72 # the normalization function can be one of the following, and is applied to
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73 # all values that correspond to the segment's label
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74 # total - sum of cell values for the segment label (row and col)
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75 # average - average of cell values for the segment label (row and col)
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76 # row_total, row_average - sum or average for cell values for the segment row
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77 # col_total, col_average - sum or average for cell values for the segment col
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78 # row_size, col_size, total_size - based on the optional size column (see col_size_row and row_size_col above)
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79 # VALUE - segments are scaled to a constant VALUE (e.g. 1000)
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80 segment_normalization_function = 1000
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81
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82 # normalization can be performed by either altering the actual data values or
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83 # by applying a visual scaling of the segments. When 'value' is used, the data
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84 # is changed. When 'visual' is used, then a chromosomes_scale line is reported
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85 # by this script which you must include in circos.conf for the scaling to be applied
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86 segment_normalization_scheme = value
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87
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88 ################################################################
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89 # placement of cell ribbons on row/column segments
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90 #
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91 # for segments that share both column and row ribbons, the
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92 # order of ribbon position can be adjusted with placement_order
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93
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94 placement_order = row,col # col,row or row,col
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95
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96 # within the row/column ribbon bundle for each segment,
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97 # ribbon_bundle_order determines how the ribbons will be
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98 # ordered
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99 # - size - by value of the cell
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100 # - ascii - sorted by destination label
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101 # - native - sorted by order of destination segment
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102
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103 ribbon_bundle_order = native # size, ascii, native
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104
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105 # reverse the position of links in table/row segments?
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106
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107 reverse_rows = no
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108 reverse_columns = no
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109
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110 # values for cells with the same row/column name can be treated
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111 # independently. You can
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112 # show - show these cells and not filter them at all
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113 # hide - hide these cells from the image, but not resize the row/columns
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114 # remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
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115 intra_cell_handling = show
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116
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117 # ribbon layering - order in which the ribbons are drawn on the image
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118 # size_asc - ascending by ribbon size (small ribbons drawn first, therefore large ribbons will be at front)
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119 # size_desc - descending by ribbon size (large ribbons drawn first, therefore small ribbons will be at front)
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120
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121 ribbon_layer_order = size_asc
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122
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123 # if both (A,B)=x and (B,A)=y cells exist, you can choose to have the ribbon
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124 # ends sized variably so that ribbon at A has width x and at B has width y
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125
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126 ribbon_variable = no
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127 ribbon_variable_intra_collapse = yes
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128
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129 ################################################################
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130 # cell value mapping allows you to remap the cell values using
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131 # any Perl expression that uses X as the cell value. For example,
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132 #
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133 # cell_remap_formula = log(X)
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134 # = sqrt(X)
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135 # = X/10
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136 # = X ? log(X) : 0
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137 #
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138 # This remapping takes place before any filters or scaling is applied. Its effect
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139 # is the same as remapping the cell values in the input file.
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140
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141 use_cell_remap = no
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142 cell_remap_formula = round(10*X)
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143
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144 ################################################################
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145 # scale your values with a power rule (useful if the range of values
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146 # is very large) to
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147 # - atten_large: attenuate large values and maintain visibility
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148 # of ribbons corresponding to small values, or
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149 # - atten_small: attenuate small values to increase visibility
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150 # of ribbons corresponding to large values
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151 #
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152 # given a value, v, and a maximum, m
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153 #
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154 # atten_small:
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155 #
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156 # v_new = m * ( exp(scale_factor * v / m) - 1 ) / ( exp(scale_factor) - 1 )
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157 #
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158 # atten_large:
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159 #
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160 # v_new = m * ( log(scale_factor * v ) ) / ( log(scale_factor * m ) )
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161 #
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162 # essentially the values are remapped to a log-type scale
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163 # with the range 0..m
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164
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165 use_scaling = no
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166 scaling_type = atten_large
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167 scale_factor = 1
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168
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169 blank_means_missing = no
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170 missing_cell_value = -
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171
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172 ################################################################
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173 # Value cutoffs for cell values and ribbon formatting.
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174 #
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175 # You can toggle the visibility of ribbons for cells outside
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176 # a min/max range. You can define one or more of these cutoffs.
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177 # The cutoffs are applied to unscaled cell values.
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178
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179 #cell_min_value = 10
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180 #cell_min_percentile = 10
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181 #cell_max_value = 100
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182 #cell_max_percentile = 100
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183
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184 # For cell values that do not pass the min/max filters above,
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185 # you can specify whether they are hidden or removed. If the
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186 # parameter is not defined, "hide" will be assumed.
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187 # hide - cell values won't be shown, but row/col will not be resized
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188 # remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
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189
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190 cutoff_cell_handling = hide
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191
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192 # The color of ribbons is by default the color of the row segment from
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193 # which they originate. The block below allows you to remap the color
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194 # of the ribbons based on cell percentile values. There are two ways
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195 # to remap colors
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196 #
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197 # - color_remap=yes, color_autoremap=no
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198 # Uses <percentile> blocks to define the percentile values and associated
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199 # color/stroke_color characteristics for ribbons. Percentile value defined
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200 # in the block (e.g. <percentile 55>) is the max percentile value for
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201 # cells associated with this block.
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202 # - color_remap=yes, color_autoremap=yes
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203 # Uses colors associated with each percentile window of size
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204 # percentile_sampling for each cell
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205
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206 <linkcolor>
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207 color_source = row
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208 percentile_source = larger
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209 color_transparency = 1
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210 color_remap = yes
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211 color_autoremap = no
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212
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213 <percentile 50>
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214 color = dgrey
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215 transparency = 5
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216 </percentile>
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217
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218 <percentile 60>
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219 color = dgrey
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220 transparency = 5
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221 </percentile>
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222
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223 <percentile 70>
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224 transparency = 1
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225 </percentile>
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226
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227 <percentile 80>
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228 transparency = 1
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229 </percentile>
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230
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231 <percentile 90>
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232 transparency = 1
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233 stroke_color = black
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234 stroke_thickness = 1p
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235 </percentile>
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236
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237 <percentile 100>
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238 transparency = 1
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239 stroke_color = black
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240 stroke_thickness = 3p
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241 </percentile>
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242
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243 </linkcolor>
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244
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245 <linkparam>
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246 color = vdgrey
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247 #stroke_color = black
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248 #stroke_thickness = 1p
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249 </linkparam>
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250
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251 # If you are using color_autoremap=yes above, then
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252 # define the percentile sampling window and
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253 # the start/end HSV color values. Percentile window
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254 # colors are interpolated between this HSV pair.
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255 #
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256 # HSV = (hue saturation value)
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257 # hue=(0..360) saturation=(0..1) value=(0..1)
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258
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259 percentile_sampling = 5
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260
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261 # count - percentile based on counts
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262 # value - percentile based on value
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263
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264 percentile_method = count
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265
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266 # use all values or only unique values when
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267 # calculating percentiles
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268 percentile_unique_only = yes
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269
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270 # use a function, f(X), to remap cell values when calculating percentiles
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271 # for the purpose of color mapping. This allows you to apply a remapping to how
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272 # colors are calculated, without actually changing the values. The remap
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273 # applies only if percentile_method=value
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274
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275 # percentile_remap = sqrt(X)
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276
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277 # Which cell value set to use for percentile color mapping
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278 # raw - original values
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279 # filtered - values that pass min/max filters
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280 # scaled - filtered values that have been scaled if use_scaling is set
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281 percentile_data_domain = raw
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282
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283 <colors>
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284 h0 = 0
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285 s0 = 1
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286 v0 = 1
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287 h1 = 300
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288 s1 = 1
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289 v1 = 1
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290 </colors>
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291
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292 # You can control the color and stroke of ribbons for each
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293 # quartile (q1, q2, q3, q4). Any values defined here will
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294 # overwrite colors determined by remapping.
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295 #
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296 # For example, if you have a lot of cells and wish to attenuate
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297 # the visibility of ribbons associated with small values, you can
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298 # set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the
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299 # ribbons into the background.
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300
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301 #cell_q1_color = vvlgrey
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302 #cell_q2_color = vlgrey
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303 #cell_q3_color = lgrey
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304 #cell_q4_color = red
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305 #cell_q1_nostroke = yes
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306 #cell_q2_nostroke = yes
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307 #cell_q3_nostroke = yes
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308 #cell_q4_nostroke = yes
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309
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310 # cell value multiplier, required when all data is small (e.g. <1), in which
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311 # case set the multiplier to something like 1000 because Circos
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312 # works only with integer scales
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313
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314 data_mult = 1
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315
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316 ################################################################
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317 # Segment labels can be optionally set to a size that is
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318 # proportional to the size of the segment. Set min/max size
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319 # values here. If this line is commented out, then the label
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320 # size is determined by the circos.conf file used to draw the image
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321
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322 #segment_label_size_range = 60,60
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323
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324 # progression controls how fast the label size changes from
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325 # min to max (larger value of progression means values close to max
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326 # are achieved for smaller segments)
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327
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328 segment_label_size_progression = 4
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329
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330 segment_label_uppercase = no
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331
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332 ################################################################
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333 # Segment colors can be specified in the data file (in this
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334 # case use row_color_col and col_color_row), otherwise colors
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335 # are interpolated within an HSV range. Color interpolation can be
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336 # done in two ways: based on segment index (interpolation steps through
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337 # colors uniformly for each segment) and total size (interpolation
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338 # steps through colors in proportion to segment size).
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339
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340 <segment_colors>
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341 interpolate_type = size # size or count
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342 h0 = 0
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343 s0 = 0.8
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344 v0 = 0.9
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345 h1 = 300
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346 s1 = 0.8
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347 v1 = 0.9
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348 </segment_colors>
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349
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350 ################################################################
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351 # Shorten the labels of segments. Specify whether to do this
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352 # with shorten_text=yes|no parameter and provide regular
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353 # expressions in string_replace which define the text to
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354 # replace.
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355
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356 shorten_text = yes
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357
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358 <string_replace>
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359 IGH =
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360 </string_replace>
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361
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362 # exit on any error
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363 strict_sanity = yes
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364
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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365 ################################################################
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366 # if the segment_prefix is set, then rows and columns will be
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367 # renamed to internal fields segment_prefix + DIGIT
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368
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369 #segment_prefix = id
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370 color_prefix = color
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371
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372 ################################################################
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
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373 # Delimiters
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374
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375 # field delimiter regular expression
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376 # if this is not defined, any whitespace will be considered a delimiter
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377 field_delim = \s
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378
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379 # collapse adjacent delimiters?
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380 field_delim_collapse = yes
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381
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382 # remove any leading space in the input file
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383 # by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table!
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384 strip_leading_space = yes
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385
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386 # remove quotes and thousand separators - concatenate characters to remove
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rhpvorderman
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387 #
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rhpvorderman
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388 # e.g. to remove characters a b c set remove_cell_rx=abc
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389 # e.g. to remove characters " ' , set remove_cell_rx="',
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390 remove_cell_rx = "',
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391