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