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