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comparison get_flanks.xml @ 0:0c66884f0cac

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:39 -0400
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1 <tool id="get_flanks1" name="Get flanks" version="0.0.1">
2 <description>returns flanking region/s for every gene</description>
3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
6 </requirements>
7 <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>
8 <inputs>
9 <param format="interval" name="input" type="data" label="Select data"/>
10 <param name="region" type="select" label="Region">
11 <option value="whole" selected="true">Whole feature</option>
12 <option value="start">Around Start</option>
13 <option value="end">Around End</option>
14 </param>
15 <param name="direction" type="select" label="Location of the flanking region/s">
16 <option value="Upstream">Upstream</option>
17 <option value="Downstream">Downstream</option>
18 <option value="Both">Both</option>
19 </param>
20 <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."/>
21 <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
22
23
24 </inputs>
25 <outputs>
26 <data format="interval" name="out_file1" metadata_source="input"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input" value="flanks_inp.bed"/>
31 <param name="offset" value="-500"/>
32 <param name="size" value="1000"/>
33 <param name="direction" value="Both"/>
34 <param name="region" value="whole"/>
35 <output name="out_file1" file="flanks_out1.bed"/>
36 </test>
37 <test>
38 <param name="input" value="flanks_inp.bed"/>
39 <param name="offset" value="200"/>
40 <param name="size" value="1000"/>
41 <param name="direction" value="Downstream"/>
42 <param name="region" value="start" />
43 <output name="out_file1" file="flanks_out2.bed"/>
44 </test>
45 </tests>
46 <help>
47
48 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
49
50 **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".
51
52 -----
53
54
55 **Example 1**
56
57 - For the following dataset::
58
59 chr22 1000 7000 NM_174568 0 +
60
61 - running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::
62
63 chr22 500 800 NM_174568 0 +
64
65 .. image:: ${static_path}/operation_icons/flanks_ex1.gif
66
67 **Example 2**
68
69 - For the following dataset::
70
71 chr22 1000 7000 NM_028946 0 -
72
73 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
74
75 chr22 500 800 NM_028946 0 -
76
77 .. image:: ${static_path}/operation_icons/flanks_ex2.gif
78
79 </help>
80
81
82 </tool>