/tools/filters/CreateInterval.xml

 1<tool id="createInterval" name="Create single interval">
 2  <description>as a new query</description>
 3  <command interpreter="perl">CreateInterval.pl $chrom $start $end "$name" $strand $out_file1</command>
 4  <inputs>
 5    <param name="chrom" size="20" type="text" value="chr7" label="Chromosome"/>
 6    <param name="start" size="20" type="integer" value="100" label="Start position"/>
 7    <param name="end"   size="20" type="integer" value="1000" label="End position"/>
 8    <param name="name" size="20" type="text" value="myInterval" label="Name"/>
 9    <param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" >
10      <option value="plus">plus</option>
11      <option value="minus">minus</option>
12    </param>    
13  </inputs>
14  <outputs>
15    <data format="bed" name="out_file1" />
16  </outputs>
17  <tests>
18    <test>
19      <param name="chrom" value="chr7"/>
20      <param name="start" value="100"/>
21      <param name="end" value="1000"/>
22      <param name="name" value="myinterval"/>
23      <param name="strand" value="plus"/>
24      <output name="out_file1" file="eq-createinterval.dat"/>
25    </test>
26  </tests>
27  <help>
28
29.. class:: warningmark
30
31**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.
32
33-----
34
35**What it does**
36
37This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.
38
39-----
40
41**Example**
42
43Typing the following values in the form::
44
45    Chromosome: chrX
46    Start position: 151087187
47    End position: 151370486
48    Name: NM_000808
49    Strand: minus
50
51will create a single interval::
52
53    chrX  151087187  151370486  NM_000808  0  -
54
55</help>
56</tool>