Mercurial > repos > iuc > gemini_windower

annotate gemini_windower.xml @ 3:e7e4a93ca32a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:45:05 -0500
parents 89783b909302
children 5b30a2213d08
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3
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Conducting analyses on genome "windows"</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">windower</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
3
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 gemini @BINARY@
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15 -w $w
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16 -s $s
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17 -t $window_analysis
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18 -o $operation
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19 "${ infile }"
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20 > "${ outfile }"
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro="infile" />
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26 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
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27 <option value="nucl_div">(nucl_div)</option>
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28 <option value="hwe">(hwe)</option>
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29 </param>
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31 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
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32 <option value="mean">mean</option>
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33 <option value="median">median</option>
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34 <option value="min">min</option>
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35 <option value="max">max</option>
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36 <option value="collapse">collapse</option>
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37 </param>
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39 <param name="w" type="integer" value="10000" label="The window size in bp"
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40 help="(-w)">
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41 <validator type="in_range" min="0"/>
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42 </param>
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43
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44 <param name="s" type="integer" value="1000" label="The step size for the windows in bp"
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45 help="(-s)">
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46 <validator type="in_range" min="0"/>
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47 </param>
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48
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49 </inputs>
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50
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51 <outputs>
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52 <data name="outfile" format="tabular" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="infile" value="gemini_windower_input.db" ftype="gemini.sqlite" />
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57 <param name="w" value="10000" />
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58 <param name="window_analysis" value="nucl_div" />
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59 <param name="operation" value="mean" />
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60 <output name="outfile" file="gemini_windower_result.tabular" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 **What it does**
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65
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66 It computs variation metrics across genomic windows (both fixed and sliding).
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67
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68 **Examples**
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69
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70 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
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71
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72 -w 50000
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73 -s 0
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74 -t nucl_div
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75 -o mean
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76
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77 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
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78
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79 -w 50000
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80 -s 10000
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81 -t nucl_div
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82 -o mean
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83
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84 Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
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85
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86 -w 10000
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87 -t hwe
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88 -o max
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89
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90 ]]></help>
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91 <expand macro="citations"/>
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92 </tool>