Mercurial > repos > iuc > resize_coordinate_window

comparison resize_coordinate_window.xml @ 0:08b6255afde7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
author iuc
date Tue, 19 Jan 2016 09:34:56 -0500
parents
children 0164d2edba9f
comparison
equal deleted inserted replaced
-1:000000000000 0:08b6255afde7
1 <tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0">
2 <description>of GFF data</description>
3 <command>
4 python $__tool_directory__/resize_coordinate_window.py
5 --input "$input"
6 --subtract_from_start $subtract_from_start
7 --add_to_end $add_to_end
8 --extend_existing $extend_existing
9 --output "$output"
10 </command>
11 <inputs>
12 <param name="input" type="data" format="gff" label="Gff file" />
13 <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/>
14 <param name="add_to_end" type="integer" value="30" min="0" label="Distance to add to the end coordinate"/>
15 <param name="extend_existing" type="select" label="Resize window from" help="The midpoint is computed as (start + end) // 2">
16 <option value="midpoint" selected="True">the midpoint of the start and end coordinates</option>
17 <option value="existing">the start and end coordinates</option>
18 </param>
19 </inputs>
20 <outputs>
21 <data name="output" format="gff" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input" value="input.gff" ftype="gff" />
26 <param name="subtract_from_start" value="13" />
27 <param name="add_to_end" value="13" />
28 <param name="extend_existing" value="midpoint" />
29 <output name="output" file="output.gff" ftype="gff" />
30 </test>
31 </tests>
32 <help>
33
34 **What it does**
35
36 Modifies the start and end coordinates of GFF data such that the new start and end position is based on a
37 specified window size that is computed either from the existing start and end coordinates or centered on
38 the midpoint between them.
39
40 -----
41
42 **Example**
43
44 If the input dataset is::
45
46 chr1 genetrack . 17 37 918 + . stddev=5.96715849116
47 chr1 genetrack . 31 51 245 - . stddev=2.66582799529
48 chr1 genetrack . 40 60 2060 + . stddev=2.7859667372
49
50 Resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces::
51
52 chr1 genetrack . 14 40 918 + . stddev=5.96715849116
53 chr1 genetrack . 28 54 245 - . stddev=2.66582799529`
54 chr1 genetrack . 37 63 2060 + . stddev=2.7859667372
55
56 </help>
57 <citations>
58 <citation type="bibtex">
59 @unpublished{None,
60 author = {},
61 title = {None},
62 year = {None},
63 eprint = {None},
64 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
65 }</citation>
66 </citations>
67 </tool>