Mercurial > repos > xuebing > sharplabtool
comparison tools/rgenetics/rgRegion.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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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> |