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