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223 lines
10 KiB
XML
223 lines
10 KiB
XML
<tool id="Cut1" name="Cut" version="1.0.2">
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<description>columns from a table</description>
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<requirements>
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<requirement type="package" version="5.26">perl</requirement>
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</requirements>
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<edam_operations>
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<edam_operation>operation_3695</edam_operation>
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</edam_operations>
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<command><![CDATA[
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perl '$__tool_directory__/cutWrapper.pl'
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'${input}'
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'${columnList}'
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${delimiter}
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'${out_file1}'
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]]></command>
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<inputs>
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<param name="columnList" type="text" value="c1,c2" label="Cut columns"/>
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<param name="delimiter" type="select" label="Delimited by">
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<option value="T">Tab</option>
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<option value="Sp">Whitespace</option>
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<option value="Dt">Dot</option>
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<option value="C">Comma</option>
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<option value="D">Dash</option>
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<option value="U">Underscore</option>
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<option value="P">Pipe</option>
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</param>
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<param name="input" type="data" format="txt" label="From"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="tabular">
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<actions>
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<conditional name="delimiter">
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<when value="T">
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<conditional name="input">
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<when datatype_isinstance="interval">
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<action type="format" default="tabular">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->
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<filter type="insert_column" column="0" value="interval"/>
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<filter type="insert_column" ref="columnList" /> <!-- startCol -->
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<filter type="insert_column" ref="columnList" /> <!-- endCol -->
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<filter type="multiple_splitter" column="1" separator=","/>
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<filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="1" name="lower" />
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<filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
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<filter type="boolean" column="1" cast="int" />
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<filter type="multiple_splitter" column="2" separator=","/>
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<filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="2" name="lower" />
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<filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
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<filter type="boolean" column="2" cast="int" />
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<filter type="multiple_splitter" column="3" separator=","/>
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<filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="3" name="lower" />
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<filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
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<filter type="boolean" column="3" cast="int" />
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<filter type="metadata_value" ref="input" name="chromCol" column="1" />
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<filter type="metadata_value" ref="input" name="startCol" column="2" />
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<filter type="metadata_value" ref="input" name="endCol" column="3" />
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</option>
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</action>
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<conditional name="out_file1">
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<when datatype_isinstance="interval">
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<action type="metadata" name="chromCol">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->
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<filter type="multiple_splitter" column="0" separator=","/>
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<filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="0" name="lower" />
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<filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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<filter type="insert_column" value="1" iterate="True" column="0"/>
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<filter type="boolean" column="1" cast="int" />
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<filter type="metadata_value" ref="input" name="chromCol" column="1" />
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</option>
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</action>
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<action type="metadata" name="startCol">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->
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<filter type="multiple_splitter" column="0" separator=","/>
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<filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="0" name="lower" />
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<filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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<filter type="insert_column" value="1" iterate="True" column="0"/>
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<filter type="boolean" column="1" cast="int" />
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<filter type="metadata_value" ref="input" name="startCol" column="1" />
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</option>
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</action>
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<action type="metadata" name="endCol">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->
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<filter type="multiple_splitter" column="0" separator=","/>
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<filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="0" name="lower" />
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<filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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<filter type="insert_column" value="1" iterate="True" column="0"/>
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<filter type="boolean" column="1" cast="int" />
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<filter type="metadata_value" ref="input" name="endCol" column="1" />
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</option>
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</action>
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<action type="metadata" name="nameCol" default="0">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->
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<filter type="multiple_splitter" column="0" separator=","/>
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<filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="0" name="lower" />
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<filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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<filter type="insert_column" value="1" iterate="True" column="0"/>
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<filter type="boolean" column="1" cast="int" />
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<filter type="metadata_value" ref="input" name="nameCol" column="1" />
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</option>
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</action>
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<action type="metadata" name="strandCol" default="0">
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<option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->
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<filter type="multiple_splitter" column="0" separator=","/>
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<filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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<filter type="string_function" column="0" name="lower" />
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<filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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<filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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<filter type="insert_column" value="1" iterate="True" column="0"/>
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<filter type="boolean" column="1" cast="int" />
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<filter type="metadata_value" ref="input" name="strandCol" column="1" />
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</option>
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</action>
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</when>
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</conditional>
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</when>
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</conditional>
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</when>
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</conditional>
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</actions>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="columnList" value="c1,c4,c2,c3"/>
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<param name="delimiter" value="T"/>
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<param name="input" value="1.bed"/>
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<output name="out_file1" file="eq-cut.dat"/>
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</test>
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<test>
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<param name="columnList" value="c1,c4,c2-c3" />
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<param name="delimiter" value="T" />
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<param name="input" value="1.bed" />
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<output name="out_file1" file="eq-cut.dat" />
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</test>
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</tests>
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<help><![CDATA[
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.. class:: warningmark
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**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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.. class:: infomark
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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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Cutting columns 1 and 3 from::
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apple,is,good
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windows,is,bad
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will give::
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apple good
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windows bad
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-----
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**What it does**
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This tool selects (cuts out) specified columns from the dataset.
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- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**
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- Columns can be specified in any order (e.g., **c2,c1,c6**)
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- If you specify more columns than actually present - empty spaces will be filled with dots
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-----
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**Example**
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Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::
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chr1 10 1000 gene1 0 +
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chr2 100 1500 gene2 0 +
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**cut** on columns "**c1,c4,c6**" will return::
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chr1 gene1 +
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chr2 gene2 +
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**cut** on columns "**c6,c5,c4,c1**" will return::
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+ 0 gene1 chr1
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+ 0 gene2 chr2
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**cut** on columns "**c1-c3**" will return::
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chr1 10 1000
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chr2 100 1500
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**cut** on columns "**c8,c7,c4**" will return::
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. . gene1
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. . gene2
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]]></help>
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</tool>
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