annotate merge_columns_with_delimiter/merge_columns_with_delimiter.xml @ 0:eaf7c9b0a1a4 draft default tip

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<tool id="merge_cols_with_delimiter1" name="Merge Columns with Delimiters" version="1.0.1">
  <description>together</description>
  <command interpreter="python">
      merge_columns_with_delimiter.py
      $input1
      $out_file1
      $delimiter
      $col1
      $col2
      #for $col in $columns
        ${col.datacol}
      #end for

  </command>
  <inputs>
    <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
    <param name="delimiter" type="select" label="Delimiter">
      <option value="s">Whitespaces</option>
      <option value="T">Tabs</option>
      <option value="Ep">EmptyString</option>
      <option value="Dt">Dots</option>
      <option value="C">Commas</option>
      <option value="D">Dashes</option>
      <option value="Sl">Left Slashes</option>
      <option value="Sr">Right Slashes</option>
      <option value="U">Underscores</option>
      <option value="P">Pipes</option>
      <option value="Co">Colons</option>
      <option value="Sc">Semicolons</option>
    </param>
    <param name="col1" label="Merge column" type="data_column" data_ref="input1" />
    <param name="col2" label="with column" type="data_column" data_ref="input1" help="Need to add more columns? Use controls below."/>

    <repeat name="columns" title="Columns">
      <param name="datacol" label="Add column" type="data_column" data_ref="input1" />
    </repeat>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="merge_columns_with_delimiter_input.tsv"/>
      <param name="delimiter" value="D" />
      <param name="col1" value="5" />
      <param name="col2" value="1" />
      <param name="datacol" value="3" />
      <output name="out_file1" file="merge_columns_with_delimiter_output.tsv"/>
    </test>
  </tests>
<help>

.. class:: infomark

**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*

-----

**What it does**

This tool merges columns together separating them with the specified delimiter.
Any number of valid columns can be merged in any order.
Tool and code inspired from 'merge_columns' tool distributed with Galaxy.

-----

**Example**

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

   1 10   1000  gene1 chr
   2 100  1500  gene2 chr

merging columns "**c5,c1**" with "-"(dash) will return::

   1 10   1000  gene1 chr chr-1
   2 100  1500  gene2 chr chr-2

.. class:: warningmark

Note that all original columns are preserved and the result of merge is added as the rightmost column.
  </help>
</tool>