Mercurial > repos > iuc > gemini_windower

annotate gemini_windower.xml @ 6:73bfda729541 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:09:47 -0500
parents 310f5bda4041
children 1c70af7be2f5
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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 <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[
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12 gemini @BINARY@
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13 -w $w
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14 -s $s
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15 -t $window_analysis
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16 -o $operation
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17 "${ infile }"
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18 > "${ outfile }"
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="infile" />
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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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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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37 <param name="w" type="integer" value="10000" 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" 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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50 <data name="outfile" format="tabular" />
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51 </outputs>
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52 <tests>
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53 <test>
5
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54 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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55 <param name="w" value="50000" />
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56 <param name="s" value="50000000" />
0
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57 <param name="window_analysis" value="nucl_div" />
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58 <param name="operation" value="mean" />
5
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59 <output name="outfile" file="gemini_windower_template.tabular" compare="re_match" />
0
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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64
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65 It computs variation metrics across genomic windows (both fixed and sliding).
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66
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67 **Examples**
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68
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69 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
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71 -w 50000
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72 -s 0
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73 -t nucl_div
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74 -o mean
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75
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76 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
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77
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78 -w 50000
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79 -s 10000
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80 -t nucl_div
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81 -o mean
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82
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83 Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
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84
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85 -w 10000
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86 -t hwe
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87 -o max
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88
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89 ]]></help>
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90 <expand macro="citations"/>
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91 </tool>