view tools/rgenetics/rgRegion.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="rgRegion" name="Subset:">
    <description>genotypes from genomic region</description>
    <command interpreter="python"> $infile $r $title $out_file1
       <param name="infile" type="data" format="lped" label="Linkage ped genotype file name from current history" size="80"/>
       <param name="title" type="text" size="80" label="Title for output files" optional="true"
        help="Descriptive title for new genotype/map files" value="RGRegion" />
       <param name="r" type="text" label="Region" help="Cut and paste a UCSC browser region" 
        size="80" value="chr9:119,506,000-122,518,000"/>
       <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" 
       <param name="outformat" type="select" label="Output file format" dynamic_options="get_rgRegionOutFormats()" size="80"/> 



       <data format="lped" name="out_file1" label="${title}.lped" metadata_source="infile" />

.. class:: infomark


- **Source** is the file you want to extract some columns from over a genomic region such as a gene or chromosome
- **Tag** is the name to give the results file for this run 
- **Region** is the genomic region cut and paste from a UCSC browser location window
- **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data



This tool is a very general purpose report builder. It can cut specific columns from 
amalgamated analyses - eg powers and pvalues,
or regressions over a specified genomic region (given as a UCSC browser location - eg)

It takes a tab delimited file containing rs chrom offset float1..floatn and cuts out a region and
a subset of the columns into a tabular file. If you make sure that RS is included, the
result that appears in your history will have a direct link to ucsc genome graphs for viewing
in full genomic context

ross lazarus (
August 2007
released under the LGPL. see documentation for license terms.