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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Conducting analyses on genome "windows"</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">windower</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 gemini @BINARY@
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12 -w $w
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13 -s $s
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14 -t $window_analysis
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15 -o $operation
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16 "${ infile }"
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17 > "${ outfile }"
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18 ]]>
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19 </command>
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20 <expand macro="stdio" />
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21 <inputs>
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2
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22 <expand macro="infile" />
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0
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23
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24 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
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25 <option value="nucl_div">(nucl_div)</option>
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26 <option value="hwe">(hwe)</option>
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27 </param>
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28
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29 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
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30 <option value="mean">mean</option>
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31 <option value="median">median</option>
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32 <option value="min">min</option>
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33 <option value="max">max</option>
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34 <option value="collapse">collapse</option>
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35 </param>
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36
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37 <param name="w" type="integer" value="10000" size="10" label="The window size in bp"
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38 help="(-w)">
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39 <validator type="in_range" min="0"/>
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40 </param>
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41
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42 <param name="s" type="integer" value="1000" size="10" label="The step size for the windows in bp"
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43 help="(-s)">
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44 <validator type="in_range" min="0"/>
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45 </param>
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46
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47 </inputs>
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48
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49 <outputs>
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2
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50 <data name="outfile" format="tabular" />
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0
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51 </outputs>
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52 <tests>
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53 <test>
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54 </test>
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55 </tests>
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56 <help>
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57 **What it does**
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58
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59 It computs variation metrics across genomic windows (both fixed and sliding).
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60
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61 @CITATION@
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62 </help>
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63 <expand macro="citations"/>
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64 </tool>
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