view tools/filters/CreateInterval.xml @ 1:cdcb0ce84a1b

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<tool id="createInterval" name="Create single interval">
  <description>as a new dataset</description>
  <command interpreter="perl">CreateInterval.pl $chrom $start $end "$name" $strand $out_file1</command>
  <inputs>
    <param name="chrom" size="20" type="text" value="chr7" label="Chromosome"/>
    <param name="start" size="20" type="integer" value="100" label="Start position"/>
    <param name="end"   size="20" type="integer" value="1000" label="End position"/>
    <param name="name" size="20" type="text" value="myInterval" label="Name"/>
    <param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" >
      <option value="plus">plus</option>
      <option value="minus">minus</option>
    </param>    
  </inputs>
  <outputs>
    <data format="bed" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="chrom" value="chr7"/>
      <param name="start" value="100"/>
      <param name="end" value="1000"/>
      <param name="name" value="myinterval"/>
      <param name="strand" value="plus"/>
      <output name="out_file1" file="eq-createinterval.dat"/>
    </test>
  </tests>
  <help>

.. class:: warningmark

**TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the "?" link in the history item.

-----

**What it does**

This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.

-----

**Example**

Typing the following values in the form::

    Chromosome: chrX
    Start position: 151087187
    End position: 151370486
    Name: NM_000808
    Strand: minus

will create a single interval::

    chrX  151087187  151370486  NM_000808  0  -

</help>
</tool>