annotate column_maker.xml @ 0:08a01b2ce4cd draft

Imported from capsule None

<tool id="Add_a_column1" name="Compute" version="1.1.0">
  <description>an expression on every row</description>
  <command interpreter="python">
    column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
  </command>
  <inputs>
    <param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>
    <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
    <param name="round" type="select" label="Round result?">
      <option value="no">NO</option>
      <option value="yes">YES</option>
    </param>    
  </inputs>
  <outputs>
    <data format="input" name="out_file1" metadata_source="input"/>
  </outputs>
  <tests>
    <test>
      <param name="cond" value="c3-c2"/>
      <param name="input" value="1.bed"/>
      <param name="round" value="no"/>
      <output name="out_file1" file="column_maker_out1.interval"/>
    </test>
    <test>
      <param name="cond" value="c4*1"/>
      <param name="input" value="1.interval"/>
      <param name="round" value="no"/>
      <output name="out_file1" file="column_maker_out2.interval"/>
    </test>
    <test>
      <param name="cond" value="c4*1"/>
      <param name="input" value="1.interval"/>
      <param name="round" value="yes"/>
      <output name="out_file1" file="column_maker_out3.interval"/>
    </test>
  </tests>
  <help>

 .. class:: infomark

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

-----

**What it does**

This tool computes an expression for every row of a dataset and appends the result as a new column (field).

- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file

- **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position

-----

**Example**

If this is your input::

   chr1  151077881  151077918  2  200  -
   chr1  151081985  151082078  3  500  +

computing "c4*c5" will produce::

   chr1  151077881  151077918  2  200  -   400.0
   chr1  151081985  151082078  3  500  +  1500.0
    
if, at the same time, "Round result?" is set to **YES** results will look like this::

   chr1  151077881  151077918  2  200  -   400
   chr1  151081985  151082078  3  500  +  1500

You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::

   chr1  151077881  151077918  2  200  -  True
   chr1  151081985  151082078  3  500  +  True

or computing "type(c2)==type('') for Input will return::

   chr1  151077881  151077918  2  200  -  False
   chr1  151081985  151082078  3  500  +  False

</help>
</tool>