Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/CreateInterval.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="createInterval" name="Create single interval"> | |
2 <description>as a new dataset</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 | |
37 This 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 | |
43 Typing 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 | |
51 will create a single interval:: | |
52 | |
53 chrX 151087187 151370486 NM_000808 0 - | |
54 | |
55 </help> | |
56 </tool> |