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/tools/rgenetics/rgRegion.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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
42This tool is a very general purpose report builder. It can cut specific columns from 
43amalgamated analyses - eg powers and pvalues,
44or regressions over a specified genomic region (given as a UCSC browser location - eg)
45
46It takes a tab delimited file containing rs chrom offset float1..floatn and cuts out a region and
47a subset of the columns into a tabular file. If you make sure that RS is included, the
48result that appears in your history will have a direct link to ucsc genome graphs for viewing
49in full genomic context
50
51ross lazarus (ross.lazarus@gmail.com)
52August 2007
53released under the LGPL. see documentation for license terms.
54
55</help>
56</tool>