root/galaxy-central/tools/rgenetics/rgRegion.xml

リビジョン 2, 2.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="rgRegion" name="Subset:">
2    <code file="rgRegion_code.py"/>
3    <code file="listFiles.py"/>
4 
5    <description>genotypes from genomic region</description>
6 
7    <command interpreter="python">
8        rgRegion.py $infile $r $tag $out_file1
9    </command>
10   
11    <inputs>   
12       <page>
13       <param name="infile" type="data" format="lped" label="Linkage ped genotype file name from current history" size="80"/>
14       <param name="r" type="text" label="Region" help="Cut and paste a UCSC browser region"
15        size="80" value="chr9:119,506,000-122,518,000"/>
16       <param name="rslist" type="text" area="true" label="List of rs numbers" help="Type (or cut and paste) a space or newline separated list of rs numbers"
17        size="5x20"/>
18
19       <param name="tag" type="text" label="Output file name" value="My_favourite_region" size="80"/>
20       <param name="outformat" type="select" label="Output file format" dynamic_options="get_rgRegionOutFormats()" size="80"/>
21        <param name="dbkey" type="hidden" value="hg18" />
22
23       </page>
24
25 
26   </inputs>
27
28   <outputs> 
29       <data format="lped" name="out_file1" />
30   </outputs>
31<help>
32
33.. class:: infomark
34
35**Syntax**
36
37- **Source** is the file you want to extract some columns from over a genomic region such as a gene or chromosome
38- **Tag** is the name to give the results file for this run
39- **Region** is the genomic region cut and paste from a UCSC browser location window
40- **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data
41
42-----
43
44**Summary**
45
46This tool is a very general purpose report builder. It can cut specific columns from
47amalgamated analyses - eg powers and pvalues,
48or regressions over a specified genomic region (given as a UCSC browser location - eg)
49
50It takes a tab delimited file containing rs chrom offset float1..floatn and cuts out a region and
51a subset of the columns into a tabular file. If you make sure that RS is included, the
52result that appears in your history will have a direct link to ucsc genome graphs for viewing
53in full genomic context
54
55ross lazarus (ross.lazarus@gmail.com)
56August 2007
57released under the LGPL. see documentation for license terms.
58
59</help>
60</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。