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1 <tool id="tp_cut_tool" name="Cut" version="0.1.1">
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1
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2 <description>columns from a table</description>
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3 <requirements>
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4 <requirement type="package" version="8.21">gnu_coreutils</requirement>
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5 </requirements>
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6 <command>
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2
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7 cut
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8 #if str($delimiter) != '':
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9 -d"${delimiter}"
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10 #end if
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11 ${complement} ${cut_element} '${list}' '${input}' > '${output}'
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12 </command>
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13
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14 <inputs>
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15 <param format="txt" name="input" type="data" label="file to cut" />
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16 <param name="complement" type="select" label="Operation">
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17 <option value="">Keep</option>
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18 <option value="--complement">Discard</option>
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19 </param>
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20
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1
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21 <param name="delimiter" type="select" label="Delimited by">
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22 <option value="">Tab</option>
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23 <option value=" ">Whitespace</option>
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24 <option value=".">Dot</option>
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25 <option value=",">Comma</option>
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26 <option value="-">Dash</option>
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27 <option value="_">Underscore</option>
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28 <option value="|">Pipe</option>
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29 </param>
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30
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31 <param name="cut_element" type="select" label="Cut by">
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32 <option value="-f">fields</option>
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33 <option value="-c">characters</option>
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34 <option value="-b">bytes</option>
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35 </param>
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36
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37 <param name="list" type="text" size="20" value="" label="List of Fields/Characters/Bytes" help="These will be kept/discarded (depending on 'operation'). <BR /> Examples: 1,3,4 or 2-5">
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38 <sanitizer>
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39 <valid initial="string.printable">
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40 <remove value="'"/>
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <!--<data format="tabular" name="output" />-->
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47 <!-- WIP, not sure that will work with the complement option -->
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48 <data format="tabular" name="output">
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49 <actions>
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50 <conditional name="cut_element">
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51 <when value="-f">
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52 <conditional name="delimiter">
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53 <when value="T">
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54 <conditional name="input">
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55 <when datatype_isinstance="interval">
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56 <action type="format" default="tabular">
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57 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1-->
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58
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59 <filter type="insert_column" column="0" value="interval"/>
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60 <filter type="insert_column" ref="list" /> <!-- startCol -->
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61 <filter type="insert_column" ref="list" /> <!-- endCol -->
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62
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63 <filter type="multiple_splitter" column="1" separator=","/>
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64 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
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65 <filter type="string_function" column="1" name="lower" />
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66 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
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67 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
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68 <filter type="boolean" column="1" cast="int" />
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69
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70 <filter type="multiple_splitter" column="2" separator=","/>
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71 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
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72 <filter type="string_function" column="2" name="lower" />
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73 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
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74 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
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75 <filter type="boolean" column="2" cast="int" />
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76
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77 <filter type="multiple_splitter" column="3" separator=","/>
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78 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
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79 <filter type="string_function" column="3" name="lower" />
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80 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
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81 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
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82 <filter type="boolean" column="3" cast="int" />
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83
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84 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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85 <filter type="metadata_value" ref="input" name="startCol" column="2" />
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86 <filter type="metadata_value" ref="input" name="endCol" column="3" />
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87
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88 </option>
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89 </action>
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90
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91 <conditional name="output">
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92 <when datatype_isinstance="interval">
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93 <action type="metadata" name="chromCol">
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94 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0-->
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95 <filter type="multiple_splitter" column="0" separator=","/>
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96 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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97 <filter type="string_function" column="0" name="lower" />
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98 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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99 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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100 <filter type="insert_column" value="1" iterate="True" column="0"/>
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101 <filter type="boolean" column="1" cast="int" />
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102 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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103 </option>
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104 </action>
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105
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106 <action type="metadata" name="startCol">
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107 <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0-->
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108 <filter type="multiple_splitter" column="0" separator=","/>
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109 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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110 <filter type="string_function" column="0" name="lower" />
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111 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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112 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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113 <filter type="insert_column" value="1" iterate="True" column="0"/>
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114 <filter type="boolean" column="1" cast="int" />
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115 <filter type="metadata_value" ref="input" name="startCol" column="1" />
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116 </option>
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117 </action>
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118
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119 <action type="metadata" name="endCol">
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120 <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0-->
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121 <filter type="multiple_splitter" column="0" separator=","/>
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122 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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123 <filter type="string_function" column="0" name="lower" />
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124 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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125 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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126 <filter type="insert_column" value="1" iterate="True" column="0"/>
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127 <filter type="boolean" column="1" cast="int" />
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128 <filter type="metadata_value" ref="input" name="endCol" column="1" />
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129 </option>
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130 </action>
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131
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132 <action type="metadata" name="nameCol" default="0">
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133 <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0-->
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134 <filter type="multiple_splitter" column="0" separator=","/>
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135 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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136 <filter type="string_function" column="0" name="lower" />
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137 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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138 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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139 <filter type="insert_column" value="1" iterate="True" column="0"/>
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140 <filter type="boolean" column="1" cast="int" />
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141 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
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142 </option>
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143 </action>
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144
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145 <action type="metadata" name="strandCol" default="0">
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146 <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0-->
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147 <filter type="multiple_splitter" column="0" separator=","/>
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148 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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149 <filter type="string_function" column="0" name="lower" />
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150 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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151 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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152 <filter type="insert_column" value="1" iterate="True" column="0"/>
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153 <filter type="boolean" column="1" cast="int" />
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154 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
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155 </option>
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156 </action>
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157 </when>
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158 </conditional>
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159
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160 </when>
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161 </conditional>
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162 </when>
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163 </conditional>
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164 </when>
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165 </conditional>
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166 </actions>
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167 </data>
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168 </outputs>
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169 <tests>
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170 <test>
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171 <param name="list" value="1,4,2,3"/>
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172 <param name="delimiter" value="T"/>
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173 <param name="input" value="1.bed"/>
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174 <output name="output" file="eq-cut.dat"/>
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175 </test>
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176 <test>
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177 <param name="list" value="1,4,2-3" />
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178 <param name="delimiter" value="T" />
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179 <param name="input" value="1.bed" />
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180 <output name="output" file="eq-cut.dat" />
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181 </test>
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182 </tests>
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183
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184 <help>
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185
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186 **What it does**
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187
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188 This tool runs the **cut** unix command, which extract or delete columns from a file.
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189
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190 -----
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191
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192 Field List Example:
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193
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194 **1,3,7** - Cut specific fields/characters.
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195
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196 **3-** - Cut from the third field/character to the end of the line.
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197
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198 **2-5** - Cut from the second to the fifth field/character.
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199
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200 **-8** - Cut from the first to the eight field/characters.
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201
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202
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203 Input Example::
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204
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205 fruit color price weight
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206 apple red 1.4 0.5
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207 orange orange 1.5 0.3
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208 banana yellow 0.9 0.3
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209
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210
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211 Output Example ( **Keeping fields 1,3,4** )::
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212
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213 fruit price weight
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214 apple 1.4 0.5
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215 orange 1.5 0.3
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216 banana 0.9 0.3
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217
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218 Output Example ( **Discarding field 2** )::
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219
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220 fruit price weight
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221 apple 1.4 0.5
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222 orange 1.5 0.3
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223 banana 0.9 0.3
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224
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225 Output Example ( **Keeping 3 characters** )::
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226
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227 fru
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228 app
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229 ora
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230 ban
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231
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232 </help>
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233 </tool>
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