root/galaxy-central/tools/regVariation/windowSplitter.xml

リビジョン 2, 3.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="winSplitter" name="Make windows">
2  <description></description>
3  <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
4  <inputs>
5    <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
6    <param format="interval" name="input" type="data" label="Select data"/>
7    <param name="size" size="10" type="integer" value="500" label="Window size"/>
8    <conditional name="wintype">
9            <param name="choice" type="select" label="Make sliding windows?">
10                <option value="0" selected="true">No</option>
11                <option value="1">Yes</option>
12                </param>
13                <when value="0">
14                <param name="offset" type="hidden" value="0" />
15        </when>
16        <when value="1">
17                <param name="offset" size="10" type="integer" value="10" label="Offset size"/>
18        </when>
19        </conditional>
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="4.bed"/>
27      <param name="size" value="5000"/>
28      <param name="choice" value="1"/>
29      <param name="offset" value="4000"/>
30      <output name="out_file1" file="4_windows.bed"/>
31    </test>
32  </tests>
33 <help>
34
35.. class:: infomark
36
37**What it does**
38
39This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
40
41-----
42
43.. class:: warningmark
44
45**Note**
46
47The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.
48
49-----
50
51.. class:: infomark
52
53**About formats**
54
55**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
56
57The first three BED fields (required) are::
58
59    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
60    2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
61    3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
62
63The additional BED fields (optional) are::
64
65    4. name - The name of the BED line.
66    5. score - A score between 0 and 1000.
67    6. strand - Defines the strand - either '+' or '-'.
68    7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
69    8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
70    9. reserved - This should always be set to zero.
71   10. blockCount - The number of blocks (exons) in the BED line.
72   11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
73   12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
74   13. expCount - The number of experiments.
75   14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
76   15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
77
78-----
79
80**Example**
81
82- For the following query::
83
84   chr22  1000  4700  NM_174568 0 +
85
86- running this tool with **Window size as 1000**,  will return::
87
88   chr22  1000  2000  NM_174568 0 +
89   chr22  2000  3000  NM_174568 0 +
90   chr22  3000  4000  NM_174568 0 +
91   
92- running this tool to make **Sliding windows** of **size 1000** and **offset 500**,  will return::
93
94   chr22  1000  2000  NM_174568 0 +
95   chr22  1500  2500  NM_174568 0 +
96   chr22  2000  3000  NM_174568 0 +
97   chr22  2500  3500  NM_174568 0 +
98   chr22  3000  4000  NM_174568 0 +
99   chr22  3500  4500  NM_174568 0 +
100 
101  </help> 
102
103
104</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。