Mercurial > repos > iuc > resize_coordinate_window
comparison resize_coordinate_window.xml @ 1:0164d2edba9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
author | iuc |
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date | Tue, 16 Feb 2016 04:05:23 -0500 |
parents | 08b6255afde7 |
children | 9ba78e8985dc |
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0:08b6255afde7 | 1:0164d2edba9f |
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1 <tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0"> | 1 <tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.1"> |
2 <description>of GFF data</description> | 2 <description>of GFF data</description> |
3 <command> | 3 <command> |
4 python $__tool_directory__/resize_coordinate_window.py | 4 python $__tool_directory__/resize_coordinate_window.py |
5 --input "$input" | 5 --input "$input" |
6 --start_coordinate $start_coordinate | |
6 --subtract_from_start $subtract_from_start | 7 --subtract_from_start $subtract_from_start |
7 --add_to_end $add_to_end | 8 --add_to_end $add_to_end |
8 --extend_existing $extend_existing | 9 --extend_existing $extend_existing |
10 --chrom_len_file ${chromInfo} | |
11 --region_boundaries $region_boundaries | |
9 --output "$output" | 12 --output "$output" |
10 </command> | 13 </command> |
11 <inputs> | 14 <inputs> |
12 <param name="input" type="data" format="gff" label="Gff file" /> | 15 <param name="input" type="data" format="gff" label="Gff file" /> |
16 <param name="start_coordinate" type="select" label="Start coordinate" help="Input data is 0-based or 1-based"> | |
17 <option value="0" selected="True">0</option> | |
18 <option value="1">1</option> | |
19 </param> | |
13 <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/> | 20 <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"/> | 21 <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"> | 22 <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> | 23 <option value="midpoint" selected="True">the midpoint of the start and end coordinates</option> |
17 <option value="existing">the start and end coordinates</option> | 24 <option value="existing">the start and end coordinates</option> |
25 </param> | |
26 <param name="region_boundaries" type="select" label="Handle chromosome boundaries by" help="Expanding the region may result in crossing chromosome start and end coordinate boundaries."> | |
27 <option value="discard" selected="True">discarding the region</option> | |
28 <option value="limit">keeping the region by limiting the expansion to not cross the start or end coordinate boundary</option> | |
29 <option value="nothing">keeping the region by allowing the expansion to cross the start or end coordinate boundary</option> | |
30 <option value="error">outputting an error</option> | |
18 </param> | 31 </param> |
19 </inputs> | 32 </inputs> |
20 <outputs> | 33 <outputs> |
21 <data name="output" format="gff" /> | 34 <data name="output" format="gff" /> |
22 </outputs> | 35 </outputs> |
23 <tests> | 36 <tests> |
24 <test> | 37 <test> |
25 <param name="input" value="input.gff" ftype="gff" /> | 38 <param name="input" value="input.gff" ftype="gff" /> |
39 <param name="start_coordinate" value="1" /> | |
26 <param name="subtract_from_start" value="13" /> | 40 <param name="subtract_from_start" value="13" /> |
27 <param name="add_to_end" value="13" /> | 41 <param name="add_to_end" value="13" /> |
28 <param name="extend_existing" value="midpoint" /> | 42 <param name="extend_existing" value="midpoint" /> |
43 <param name="region_boundaries" value="error" /> | |
29 <output name="output" file="output.gff" ftype="gff" /> | 44 <output name="output" file="output.gff" ftype="gff" /> |
45 </test> | |
46 <test> | |
47 <param name="input" value="input.gff" ftype="gff" /> | |
48 <param name="start_coordinate" value="0" /> | |
49 <param name="subtract_from_start" value="80" /> | |
50 <param name="add_to_end" value="80" /> | |
51 <param name="extend_existing" value="midpoint" /> | |
52 <param name="region_boundaries" value="discard" /> | |
53 <output name="output" file="output_discard.gff" ftype="gff" /> | |
30 </test> | 54 </test> |
31 </tests> | 55 </tests> |
32 <help> | 56 <help> |
33 | 57 |
34 **What it does** | 58 **What it does** |
35 | 59 |
36 Modifies the start and end coordinates of GFF data such that the new start and end position is based on a | 60 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 | 61 specified region size that is computed either from the existing start and end coordinates or centered on |
38 the midpoint between them. | 62 the midpoint between them. |
63 | |
64 Region expansion may result in the new start or end coordinates crossing the chromosome boundary. The | |
65 chromosome start is set to 0 or 1 using the **Start coordinate** parameter. The end is retrieved from a | |
66 file within the Galaxy environment that includes the length of chromosomes for all genome builds. If these | |
67 files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit | |
68 integer. The **Handle chromosome boundaries by** parameter handles chromosome boundaries that are crossed | |
69 by expanding the region using one of the following options. | |
70 | |
71 * **discarding the region** - the region will be discarded and processing will continue with the next line in the dataset. | |
72 * **keeping the region by limiting the expansion to not cross the start or end coordinate boundary** - expansion will be restricted to not cross the chromosome's start or end coordinates for the current region. | |
73 * **keeping the region by allowing the expansion to cross the start or end coordinate boundary** - allow defined expansion, crossing the start boundary results in a negative start value. | |
74 * **outputting an error** - Stop processing and display an error. | |
39 | 75 |
40 ----- | 76 ----- |
41 | 77 |
42 **Example** | 78 **Example** |
43 | 79 |
45 | 81 |
46 chr1 genetrack . 17 37 918 + . stddev=5.96715849116 | 82 chr1 genetrack . 17 37 918 + . stddev=5.96715849116 |
47 chr1 genetrack . 31 51 245 - . stddev=2.66582799529 | 83 chr1 genetrack . 31 51 245 - . stddev=2.66582799529 |
48 chr1 genetrack . 40 60 2060 + . stddev=2.7859667372 | 84 chr1 genetrack . 40 60 2060 + . stddev=2.7859667372 |
49 | 85 |
50 Resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces:: | 86 Setting start coordinate to 1 and resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces:: |
51 | 87 |
52 chr1 genetrack . 14 40 918 + . stddev=5.96715849116 | 88 chr1 genetrack . 14 40 918 + . stddev=5.96715849116 |
53 chr1 genetrack . 28 54 245 - . stddev=2.66582799529` | 89 chr1 genetrack . 28 54 245 - . stddev=2.66582799529` |
54 chr1 genetrack . 37 63 2060 + . stddev=2.7859667372 | 90 chr1 genetrack . 37 63 2060 + . stddev=2.7859667372 |
55 | 91 |
56 </help> | 92 </help> |
57 <citations> | 93 <citations> |
58 <citation type="bibtex"> | 94 <citation type="bibtex"> |
59 @unpublished{None, | 95 @unpublished{None, |
60 author = {}, | 96 author = {Greg Von Kuster}, |
61 title = {None}, | 97 title = {None}, |
62 year = {None}, | 98 year = {None}, |
63 eprint = {None}, | 99 eprint = {None}, |
64 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} | 100 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} |
65 }</citation> | 101 }</citation> |