root/galaxy-central/tools/new_operations/get_flanks.xml

リビジョン 2, 3.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="get_flanks1" name="Get flanks">
2  <description>returns flanking region/s for every gene</description>
3  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
4  <inputs>
5    <param format="interval" name="input" type="data" label="Select data"/>
6    <param name="region" type="select" label="Region">
7      <option value="whole" selected="true">Whole feature</option>
8      <option value="start">Around Start</option>
9      <option value="end">Around End</option>
10    </param>
11    <param name="direction" type="select" label="Location of the flanking region/s">
12      <option value="Upstream">Upstream</option>
13      <option value="Downstream">Downstream</option>
14      <option value="Both">Both</option>
15    </param>
16    <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
17    <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
18   
19   
20  </inputs>
21  <outputs>
22    <data format="interval" name="out_file1" metadata_source="input"/>
23  </outputs>
24  <tests>
25    <test>
26      <param name="input" value="flanks_inp.bed"/>
27      <param name="offset" value="-500"/>
28      <param name="size" value="1000"/>
29      <param name="direction" value="Both"/>
30      <param name="region" value="whole"/>
31      <output name="out_file1" file="flanks_out1.bed"/>
32    </test>
33    <test>
34      <param name="input" value="flanks_inp.bed"/>
35      <param name="offset" value="200"/>
36      <param name="size" value="1000"/>
37      <param name="direction" value="Downstream"/>
38      <param name="region" value="start" />
39      <output name="out_file1" file="flanks_out2.bed"/>
40    </test>
41  </tests>
42 <help>
43
44This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
45
46**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
47
48-----
49
50
51**Example 1**
52
53- For the following query::
54
55   chr22  1000  7000  NM_174568 0 +
56
57- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
58
59   chr22  500  800  NM_174568 0 +
60
61.. image:: ../static/operation_icons/flanks_ex1.gif
62
63**Example 2**
64
65- For the following query::
66
67   chr22  1000  7000  NM_028946 0 -
68
69- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
70
71   chr22  500  800  NM_028946 0 -
72
73.. image:: ../static/operation_icons/flanks_ex2.gif
74
75</help> 
76
77
78</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。