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