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1 <tool id="Cut1" name="Cut" version="1.0.1">
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2 <description>columns from a table</description>
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3 <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command>
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4 <inputs>
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5 <param name="columnList" size="10" type="text" value="c1,c2" label="Cut columns"/>
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6 <param name="delimiter" type="select" label="Delimited by">
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7 <option value="T">Tab</option>
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8 <option value="Sp">Whitespace</option>
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9 <option value="Dt">Dot</option>
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10 <option value="C">Comma</option>
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11 <option value="D">Dash</option>
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12 <option value="U">Underscore</option>
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13 <option value="P">Pipe</option>
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14 </param>
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15 <param format="txt" name="input" type="data" label="From"/>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="out_file1" >
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19 <actions>
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20 <conditional name="delimiter">
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21 <when value="T">
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22 <conditional name="input">
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23 <when datatype_isinstance="interval">
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24 <action type="format" default="tabular">
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25 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->
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26
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27 <filter type="insert_column" column="0" value="interval"/>
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28
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29 <filter type="insert_column" ref="columnList" /> <!-- startCol -->
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30
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31 <filter type="insert_column" ref="columnList" /> <!-- endCol -->
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32
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33 <filter type="multiple_splitter" column="1" separator=","/>
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34 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
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35 <filter type="string_function" column="1" name="lower" />
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36 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
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37 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
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38 <filter type="boolean" column="1" cast="int" />
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39
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40 <filter type="multiple_splitter" column="2" separator=","/>
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41 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
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42 <filter type="string_function" column="2" name="lower" />
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43 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
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44 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
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45 <filter type="boolean" column="2" cast="int" />
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46
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47 <filter type="multiple_splitter" column="3" separator=","/>
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48 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
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49 <filter type="string_function" column="3" name="lower" />
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50 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
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51 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
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52 <filter type="boolean" column="3" cast="int" />
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53
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54 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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55 <filter type="metadata_value" ref="input" name="startCol" column="2" />
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56 <filter type="metadata_value" ref="input" name="endCol" column="3" />
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57
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58 </option>
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59 </action>
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60
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61 <conditional name="out_file1">
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62 <when datatype_isinstance="interval">
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63 <action type="metadata" name="chromCol">
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64 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->
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65 <filter type="multiple_splitter" column="0" separator=","/>
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66 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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67 <filter type="string_function" column="0" name="lower" />
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68 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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69 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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70 <filter type="insert_column" value="1" iterate="True" column="0"/>
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71 <filter type="boolean" column="1" cast="int" />
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72 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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73 </option>
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74 </action>
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75
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76 <action type="metadata" name="startCol">
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77 <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->
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78 <filter type="multiple_splitter" column="0" separator=","/>
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79 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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80 <filter type="string_function" column="0" name="lower" />
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81 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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82 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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83 <filter type="insert_column" value="1" iterate="True" column="0"/>
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84 <filter type="boolean" column="1" cast="int" />
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85 <filter type="metadata_value" ref="input" name="startCol" column="1" />
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86 </option>
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87 </action>
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88
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89 <action type="metadata" name="endCol">
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90 <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->
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91 <filter type="multiple_splitter" column="0" separator=","/>
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92 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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93 <filter type="string_function" column="0" name="lower" />
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94 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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95 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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96 <filter type="insert_column" value="1" iterate="True" column="0"/>
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97 <filter type="boolean" column="1" cast="int" />
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98 <filter type="metadata_value" ref="input" name="endCol" column="1" />
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99 </option>
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100 </action>
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101
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102 <action type="metadata" name="nameCol" default="0">
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103 <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->
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104 <filter type="multiple_splitter" column="0" separator=","/>
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105 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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106 <filter type="string_function" column="0" name="lower" />
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107 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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108 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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109 <filter type="insert_column" value="1" iterate="True" column="0"/>
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110 <filter type="boolean" column="1" cast="int" />
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111 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
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112 </option>
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113 </action>
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114
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115 <action type="metadata" name="strandCol" default="0">
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116 <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->
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117 <filter type="multiple_splitter" column="0" separator=","/>
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118 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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119 <filter type="string_function" column="0" name="lower" />
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120 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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121 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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122 <filter type="insert_column" value="1" iterate="True" column="0"/>
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123 <filter type="boolean" column="1" cast="int" />
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124 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
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125 </option>
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126 </action>
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127 </when>
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128 </conditional>
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129
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130 </when>
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131 </conditional>
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132 </when>
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133 </conditional>
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134 </actions>
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135 </data>
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136 </outputs>
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137 <tests>
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138 <test>
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139 <param name="columnList" value="c1,c4,c2,c3"/>
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140 <param name="delimiter" value="T"/>
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141 <param name="input" value="1.bed"/>
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142 <output name="out_file1" file="eq-cut.dat"/>
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143 </test>
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144 </tests>
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145 <help>
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146
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147 .. class:: warningmark
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148
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149 **WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item.
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150
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151 .. class:: infomark
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152
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153 The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example:
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154
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155 Cutting columns 1 and 3 from::
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156
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157 apple,is,good
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158 windows,is,bad
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159
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160 will give::
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161
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162 apple good
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163 windows bad
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164
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165 -----
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166
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167 **What it does**
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168
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169 This tool selects (cuts out) specified columns from the dataset.
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170
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171 - Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**
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172 - Columns can be specified in any order (e.g., **c2,c1,c6**)
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173 - If you specify more columns than actually present - empty spaces will be filled with dots
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174
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175 -----
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176
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177 **Example**
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178
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179 Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::
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180
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181 chr1 10 1000 gene1 0 +
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182 chr2 100 1500 gene2 0 +
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183
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184 **cut** on columns "**c1,c4,c6**" will return::
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185
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186 chr1 gene1 +
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187 chr2 gene2 +
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188
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189 **cut** on columns "**c6,c5,c4,c1**" will return::
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190
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191 + 0 gene1 chr1
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192 + 0 gene2 chr2
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193
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194
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195 **cut** on columns "**c8,c7,c4**" will return::
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196
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197 . . gene1
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198 . . gene2
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199
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200
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201 </help>
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202 </tool>
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