annotate tools/new_operations/get_flanks.xml @ 0:9071e359b9a3

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<tool id="get_flanks1" name="Get flanks">
  <description>returns flanking region/s for every gene</description>
  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
  <inputs>
    <param format="interval" name="input" type="data" label="Select data"/>
    <param name="region" type="select" label="Region">
      <option value="whole" selected="true">Whole feature</option>
      <option value="start">Around Start</option>
      <option value="end">Around End</option>
    </param>
    <param name="direction" type="select" label="Location of the flanking region/s">
      <option value="Upstream">Upstream</option>
      <option value="Downstream">Downstream</option>
      <option value="Both">Both</option>
    </param>
    <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
    <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
    
    
  </inputs>
  <outputs>
    <data format="interval" name="out_file1" metadata_source="input"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="flanks_inp.bed"/>
      <param name="offset" value="-500"/>
      <param name="size" value="1000"/>
      <param name="direction" value="Both"/>
      <param name="region" value="whole"/>
      <output name="out_file1" file="flanks_out1.bed"/>
    </test>
    <test>
      <param name="input" value="flanks_inp.bed"/>
      <param name="offset" value="200"/>
      <param name="size" value="1000"/>
      <param name="direction" value="Downstream"/>
      <param name="region" value="start" />
      <output name="out_file1" file="flanks_out2.bed"/>
    </test>
  </tests>
 <help> 

This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 

**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".

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**Example 1**

- For the following query::

   chr22  1000  7000  NM_174568 0 +

- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::

   chr22  500  800  NM_174568 0 +

.. image:: ./static/operation_icons/flanks_ex1.gif

**Example 2**

- For the following query::

   chr22  1000  7000  NM_028946 0 -

- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::

   chr22  500  800  NM_028946 0 -

.. image:: ./static/operation_icons/flanks_ex2.gif

</help>  


</tool>