[2] | 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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