Mercurial > repos > iuc > gemini_windower

annotate gemini_windower.xml @ 8:406d3552beca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:27:41 +0000
parents 3b5b1ebc8423
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Compute sliding window statistics from variants</description>
8
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3 <expand macro="bio_tools"/>
0
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">windower</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 gemini @BINARY@
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14 -w $w
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15 -s $s
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16 -t $window_analysis
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17 -o $operation
5
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18 '$infile'
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19 > '$outfile'
0
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20 ]]>
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21 </command>
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22 <inputs>
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23 <expand macro="infile" />
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24
5
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25 <param argument="-t" name="window_analysis" type="select"
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26 label="The type of window analysis requested?" help="">
0
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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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30
5
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31 <param argument="-o" name="operation" type="select"
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32 label="The operation that should be applied to the -t values" help="">
0
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33 <option value="mean">mean</option>
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34 <option value="median">median</option>
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35 <option value="min">min</option>
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36 <option value="max">max</option>
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37 <option value="collapse">collapse</option>
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38 </param>
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39
5
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40 <param argument="-w" name="w" type="integer" value="10000" min="2"
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41 label="Window size in bp" help="" />
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42 <param argument="-s" name="s" type="integer" value="1000" min="0"
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43 label="Step size for sliding the window in bp" help="Specify 0 here for sliding by one full window size" />
0
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44 </inputs>
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45 <outputs>
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46 <data name="outfile" format="tabular" />
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47 </outputs>
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48 <tests>
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49 <test>
4
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50 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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51 <param name="w" value="50000" />
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52 <param name="s" value="50000000" />
0
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53 <param name="window_analysis" value="nucl_div" />
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54 <param name="operation" value="mean" />
4
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55 <output name="outfile" file="gemini_windower_template.tabular" compare="re_match" />
0
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 **What it does**
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60
5
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61 Compute variation metrics across genomic windows.
0
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62
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63 **Examples**
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64
5
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65 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows::
0
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66
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67 -w 50000
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68 -s 0
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69 -t nucl_div
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70 -o mean
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71
5
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72 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb::
0
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73
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74 -w 50000
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75 -s 10000
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76 -t nucl_div
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77 -o mean
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78
5
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79 Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome::
0
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80
5
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81 -w 10000
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82 -s 100000
0
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83 -t hwe
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84 -o max
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85
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86 ]]></help>
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87 <expand macro="citations"/>
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88 </tool>