mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
57 lines
1.7 KiB
XML
57 lines
1.7 KiB
XML
<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>
|