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comparison tools/new_operations/get_flanks.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
44 This 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>