annotate mergeCols.xml @ 1:f2aac0c5c60d

Added quotes and brackets to appropriate command arguments

<tool id="mergeCols1" name="Merge Columns" version="1.0.1">
  <description>together</description>
  <command interpreter="python">
   mergeCols.py 
      "${input1}"
      "${out_file1}"
      "${col1}"
      "${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="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="1.bed"/>
      <param name="col1" value="4" />
      <param name="col2" value="1" />
      <param name="datacol" value="6" />
      <output name="out_file1" file="mergeCols.dat"/>
    </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. Any number of valid columns can be merged in any order.

-----

**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**" will return::

   1 10   1000  gene1 chr chr1
   2 100  1500  gene2 chr chr2

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