<tool id="Cut1" name="Cut" version="1.0.2">

  <description>columns from a table</description>

  <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command>

  <inputs>

    <param name="columnList" size="10" type="text" value="c1,c2" label="Cut columns"/>

    <param name="delimiter" type="select" label="Delimited by">

      <option value="T">Tab</option>

      <option value="Sp">Whitespace</option>

      <option value="Dt">Dot</option>

      <option value="C">Comma</option>

      <option value="D">Dash</option>

      <option value="U">Underscore</option>

      <option value="P">Pipe</option>

    </param>

    <param format="txt" name="input" type="data" label="From"/>

  </inputs>

  <outputs>

    <data format="tabular" name="out_file1" >

      <actions>

        <conditional name="delimiter">

          <when value="T">

            <conditional name="input">

              <when datatype_isinstance="interval">

                <action type="format" default="tabular">

                  <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->

                    

                    <filter type="insert_column" column="0" value="interval"/>

                    

                    <filter type="insert_column" ref="columnList" /> <!-- startCol -->

                    

                    <filter type="insert_column" ref="columnList" /> <!-- endCol -->

                    

                    <filter type="multiple_splitter" column="1" separator=","/>

                    <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->

                    <filter type="string_function" column="1" name="lower" />

                    <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>

                    <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's  -->

                    <filter type="boolean" column="1" cast="int" />

                    

                    <filter type="multiple_splitter" column="2" separator=","/>

                    <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->

                    <filter type="string_function" column="2" name="lower" />

                    <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>

                    <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's  -->

                    <filter type="boolean" column="2" cast="int" />

                    

                    <filter type="multiple_splitter" column="3" separator=","/>

                    <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->

                    <filter type="string_function" column="3" name="lower" />

                    <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>

                    <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's  -->

                    <filter type="boolean" column="3" cast="int" />

                    

                    <filter type="metadata_value" ref="input" name="chromCol" column="1" />

                    <filter type="metadata_value" ref="input" name="startCol" column="2" />

                    <filter type="metadata_value" ref="input" name="endCol" column="3" />

                    

                  </option>

                </action>

                

                <conditional name="out_file1">

                  <when datatype_isinstance="interval">

                    <action type="metadata" name="chromCol">

                      <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->

                        <filter type="multiple_splitter" column="0" separator=","/>

                        <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->

                        <filter type="string_function" column="0" name="lower" />

                        <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>

                        <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's  -->

                        <filter type="insert_column" value="1" iterate="True" column="0"/>

                        <filter type="boolean" column="1" cast="int" /> 

                        <filter type="metadata_value" ref="input" name="chromCol" column="1" />

                      </option>

                    </action>

                    

                    <action type="metadata" name="startCol">

                      <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->

                        <filter type="multiple_splitter" column="0" separator=","/>

                        <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->

                        <filter type="string_function" column="0" name="lower" />

                        <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>

                        <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's  -->

                        <filter type="insert_column" value="1" iterate="True" column="0"/>

                        <filter type="boolean" column="1" cast="int" />

                        <filter type="metadata_value" ref="input" name="startCol" column="1" />

                      </option>

                    </action>

                    

                    <action type="metadata" name="endCol">

                      <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->

                        <filter type="multiple_splitter" column="0" separator=","/>

                        <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->

                        <filter type="string_function" column="0" name="lower" />

                        <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>

                        <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's  -->

                        <filter type="insert_column" value="1" iterate="True" column="0"/>

                        <filter type="boolean" column="1" cast="int" />

                        <filter type="metadata_value" ref="input" name="endCol" column="1" />

                      </option>

                    </action>

                  

                    <action type="metadata" name="nameCol" default="0">

                      <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->

                        <filter type="multiple_splitter" column="0" separator=","/>

                        <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->

                        <filter type="string_function" column="0" name="lower" />

                        <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>

                        <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's  -->

                        <filter type="insert_column" value="1" iterate="True" column="0"/>

                        <filter type="boolean" column="1" cast="int" />

                        <filter type="metadata_value" ref="input" name="nameCol" column="1" />

                      </option>

                    </action>

                  

                    <action type="metadata" name="strandCol" default="0">

                      <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->

                        <filter type="multiple_splitter" column="0" separator=","/>

                        <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->

                        <filter type="string_function" column="0" name="lower" />

                        <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>

                        <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's  -->

                        <filter type="insert_column" value="1" iterate="True" column="0"/>

                        <filter type="boolean" column="1" cast="int" />

                        <filter type="metadata_value" ref="input" name="strandCol" column="1" />

                      </option>

                    </action>  

                  </when>

                </conditional>

                

              </when>

            </conditional>

          </when>

        </conditional>

      </actions>

    </data>

  </outputs>

  <tests>

    <test>

      <param name="columnList" value="c1,c4,c2,c3"/>

      <param name="delimiter" value="T"/>

      <param name="input" value="1.bed"/>

      <output name="out_file1" file="eq-cut.dat"/>

    </test>

    <test>

      <param name="columnList" value="c1,c4,c2-c3" />

      <param name="delimiter" value="T" />

      <param name="input" value="1.bed" />

      <output name="out_file1" file="eq-cut.dat" />

    </test>

  </tests>

  <help>



.. class:: warningmark



**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.



.. class:: infomark



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:



  Cutting columns 1 and 3 from::



     apple,is,good

     windows,is,bad



  will give::



    apple   good

    windows bad



-----



**What it does**



This tool selects (cuts out) specified columns from the dataset.



- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**

- Columns can be specified in any order (e.g., **c2,c1,c6**)

- If you specify more columns than actually present - empty spaces will be filled with dots



-----



**Example**



Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::



   chr1 10   1000  gene1 0 +

   chr2 100  1500  gene2 0 +



**cut** on columns "**c1,c4,c6**" will return::



   chr1 gene1 +

   chr2 gene2 +



**cut** on columns "**c6,c5,c4,c1**" will return::



   + 0 gene1 chr1 

   + 0 gene2 chr2



**cut** on columns "**c1-c3**" will return::



   chr1 10   1000 

   chr2 100  1500





**cut** on columns "**c8,c7,c4**" will return::



   . . gene1 

   . . gene2

   



</help>

</tool>