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1 <tool id="tp_cut_tool" name="Cut" version="@BASE_VERSION@.0">
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2 <description>columns from a table</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 <version_command>cut --version | head -n 1</version_command>
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8 <command>
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9 <![CDATA[
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10 cut
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11 #if str($delimiter) != '':
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12 -d"${delimiter}"
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13 #end if
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14 ${complement}
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15 ${cut_type_options.cut_element}
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16 '${cut_type_options.list}'
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17 '${input}'
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18 > '${output}'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="input" format="txt" type="data" label="File to cut" />
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23 <param name="complement" type="select" label="Operation">
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24 <option value="">Keep</option>
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25 <option value="--complement">Discard</option>
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26 </param>
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27 <param name="delimiter" type="select" label="Delimited by">
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28 <option value="">Tab</option>
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29 <option value=" ">Whitespace</option>
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30 <option value=".">Dot</option>
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31 <option value=",">Comma</option>
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32 <option value="-">Dash</option>
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33 <option value="_">Underscore</option>
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34 <option value="|">Pipe</option>
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35 </param>
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36 <conditional name="cut_type_options">
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37 <param name="cut_element" type="select" label="Cut by">
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38 <option value="-f">fields</option>
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39 <option value="-c">characters</option>
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40 <option value="-b">bytes</option>
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41 </param>
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42 <when value="-f">
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43 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
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44 </when>
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45 <when value="-c">
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46 <param name="list" type="text" size="20" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). <BR /> Examples: 1,3,4 or 2-5">
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47 <sanitizer>
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48 <valid initial="string.printable">
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49 <remove value="'"/>
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50 </valid>
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51 </sanitizer>
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52 </param>
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53 </when>
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54 <when value="-b">
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55 <param name="list" type="text" size="20" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). <BR /> Examples: 1,3,4 or 2-5">
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56 <sanitizer>
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57 <valid initial="string.printable">
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58 <remove value="'"/>
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59 </valid>
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60 </sanitizer>
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61 </param>
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <!--<data format="tabular" name="output" />-->
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67 <!-- WIP, not sure that will work with the complement option -->
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68 <data format="tabular" name="output">
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69 <actions>
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70 <conditional name="cut_type_options.cut_element">
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71 <!-- fields -->
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72 <when value="-f">
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73 <conditional name="delimiter">
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74 <when value="T">
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75 <conditional name="input">
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76 <when datatype_isinstance="interval">
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77 <action type="format" default="tabular">
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78 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1-->
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79 <filter type="insert_column" column="0" value="interval"/>
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80 <filter type="insert_column" ref="list" /> <!-- startCol -->
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81 <filter type="insert_column" ref="list" /> <!-- endCol -->
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82
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83 <filter type="multiple_splitter" column="1" separator=","/>
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84 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
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85 <filter type="string_function" column="1" name="lower" />
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86 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
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87 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
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88 <filter type="boolean" column="1" cast="int" />
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89
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90 <filter type="multiple_splitter" column="2" separator=","/>
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91 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
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92 <filter type="string_function" column="2" name="lower" />
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93 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
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94 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
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95 <filter type="boolean" column="2" cast="int" />
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96
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97 <filter type="multiple_splitter" column="3" separator=","/>
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98 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
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99 <filter type="string_function" column="3" name="lower" />
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100 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
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101 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
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102 <filter type="boolean" column="3" cast="int" />
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103
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104 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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105 <filter type="metadata_value" ref="input" name="startCol" column="2" />
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106 <filter type="metadata_value" ref="input" name="endCol" column="3" />
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107 </option>
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108 </action>
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109 <conditional name="output">
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110 <when datatype_isinstance="interval">
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111 <action type="metadata" name="chromCol">
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112 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0-->
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113 <filter type="multiple_splitter" column="0" separator=","/>
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114 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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115 <filter type="string_function" column="0" name="lower" />
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116 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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117 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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118 <filter type="insert_column" value="1" iterate="True" column="0"/>
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119 <filter type="boolean" column="1" cast="int" />
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120 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
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121 </option>
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122 </action>
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123
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124 <action type="metadata" name="startCol">
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125 <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0-->
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126 <filter type="multiple_splitter" column="0" separator=","/>
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127 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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128 <filter type="string_function" column="0" name="lower" />
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129 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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130 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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131 <filter type="insert_column" value="1" iterate="True" column="0"/>
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132 <filter type="boolean" column="1" cast="int" />
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133 <filter type="metadata_value" ref="input" name="startCol" column="1" />
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134 </option>
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135 </action>
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136
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137 <action type="metadata" name="endCol">
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138 <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0-->
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139 <filter type="multiple_splitter" column="0" separator=","/>
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140 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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141 <filter type="string_function" column="0" name="lower" />
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142 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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143 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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144 <filter type="insert_column" value="1" iterate="True" column="0"/>
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145 <filter type="boolean" column="1" cast="int" />
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146 <filter type="metadata_value" ref="input" name="endCol" column="1" />
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147 </option>
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148 </action>
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149
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150 <action type="metadata" name="nameCol" default="0">
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151 <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0-->
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152 <filter type="multiple_splitter" column="0" separator=","/>
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153 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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154 <filter type="string_function" column="0" name="lower" />
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155 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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156 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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157 <filter type="insert_column" value="1" iterate="True" column="0"/>
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158 <filter type="boolean" column="1" cast="int" />
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159 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
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160 </option>
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161 </action>
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162
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163 <action type="metadata" name="strandCol" default="0">
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164 <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0-->
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165 <filter type="multiple_splitter" column="0" separator=","/>
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166 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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167 <filter type="string_function" column="0" name="lower" />
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168 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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169 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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170 <filter type="insert_column" value="1" iterate="True" column="0"/>
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171 <filter type="boolean" column="1" cast="int" />
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172 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
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173 </option>
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174 </action>
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175 </when>
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176 </conditional>
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177 </when>
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178 </conditional>
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179 </when>
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180 </conditional>
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181 </when>
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182 </conditional>
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183 </actions>
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184 </data>
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185 </outputs>
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186 <tests>
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187 <test>
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188 <param name="input" value="cut1.txt"/>
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189 <param name="list" value="1,3,4"/>
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190 <param name="delimiter" value=""/>
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191 <output name="output" file="cut_results1.txt"/>
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192 </test>
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193 <test>
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194 <param name="input" value="cut1.txt"/>
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195 <param name="list" value="2" />
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196 <param name="delimiter" value="" />
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197 <param name="complement" value="--complement" />
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198 <output name="output" file="cut_results2.txt"/>
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199 </test>
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200 <test>
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201 <param name="input" value="cut1.txt"/>
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202 <param name="list" value="-3" />
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203 <param name="delimiter" value="" />
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204 <param name="cut_element" value="-c" />
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205 <output name="output" file="cut_results3.txt"/>
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206 </test>
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207 </tests>
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208 <help>
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209 <![CDATA[
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210 **What it does**
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211
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212 This tool runs the **cut** unix command, which extract or delete columns from a file.
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213
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214 -----
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215
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216 Field List Example:
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217
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218 **1,3,7** - Cut specific fields/characters.
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219
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220 **3-** - Cut from the third field/character to the end of the line.
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221
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222 **2-5** - Cut from the second to the fifth field/character.
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223
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224 **-8** - Cut from the first to the eight field/characters.
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225
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226
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227 Input Example::
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228
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229 fruit color price weight
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230 apple red 1.4 0.5
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231 orange orange 1.5 0.3
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232 banana yellow 0.9 0.3
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233
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234
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235 Output Example ( **Keeping fields 1,3,4** )::
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236
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237 fruit price weight
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238 apple 1.4 0.5
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239 orange 1.5 0.3
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240 banana 0.9 0.3
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241
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242 Output Example ( **Discarding field 2** )::
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243
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244 fruit price weight
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245 apple 1.4 0.5
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246 orange 1.5 0.3
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247 banana 0.9 0.3
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248
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249 Output Example ( **Keeping 3 characters** )::
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250
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251 fru
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252 app
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253 ora
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254 ban
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255
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256 @REFERENCES@
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257 ]]>
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258 </help>
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259 </tool>
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