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comparison gemini_windower.xml @ 7:1c70af7be2f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:19:33 -0500
parents 73bfda729541
children 2e5301f3b2a4
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6:73bfda729541 7:1c70af7be2f5
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
2 <description>Conducting analyses on genome "windows"</description> 2 <description>Compute sliding window statistics from variants</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">windower</token> 5 <token name="@BINARY@">windower</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
12 gemini @BINARY@ 12 gemini @BINARY@
13 -w $w 13 -w $w
14 -s $s 14 -s $s
15 -t $window_analysis 15 -t $window_analysis
16 -o $operation 16 -o $operation
17 "${ infile }" 17 '$infile'
18 > "${ outfile }" 18 > '$outfile'
19 ]]> 19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <expand macro="infile" /> 22 <expand macro="infile" />
23 23
24 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)"> 24 <param argument="-t" name="window_analysis" type="select"
25 label="The type of window analysis requested?" help="">
25 <option value="nucl_div">(nucl_div)</option> 26 <option value="nucl_div">(nucl_div)</option>
26 <option value="hwe">(hwe)</option> 27 <option value="hwe">(hwe)</option>
27 </param> 28 </param>
28 29
29 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)"> 30 <param argument="-o" name="operation" type="select"
31 label="The operation that should be applied to the -t values" help="">
30 <option value="mean">mean</option> 32 <option value="mean">mean</option>
31 <option value="median">median</option> 33 <option value="median">median</option>
32 <option value="min">min</option> 34 <option value="min">min</option>
33 <option value="max">max</option> 35 <option value="max">max</option>
34 <option value="collapse">collapse</option> 36 <option value="collapse">collapse</option>
35 </param> 37 </param>
36 38
37 <param name="w" type="integer" value="10000" label="The window size in bp" 39 <param argument="-w" name="w" type="integer" value="10000" min="2"
38 help="(-w)"> 40 label="Window size in bp" help="" />
39 <validator type="in_range" min="0"/> 41 <param argument="-s" name="s" type="integer" value="1000" min="0"
40 </param> 42 label="Step size for sliding the window in bp" help="Specify 0 here for sliding by one full window size" />
41
42 <param name="s" type="integer" value="1000" label="The step size for the windows in bp"
43 help="(-s)">
44 <validator type="in_range" min="0"/>
45 </param>
46
47 </inputs> 43 </inputs>
48
49 <outputs> 44 <outputs>
50 <data name="outfile" format="tabular" /> 45 <data name="outfile" format="tabular" />
51 </outputs> 46 </outputs>
52 <tests> 47 <tests>
53 <test> 48 <test>
60 </test> 55 </test>
61 </tests> 56 </tests>
62 <help><![CDATA[ 57 <help><![CDATA[
63 **What it does** 58 **What it does**
64 59
65 It computs variation metrics across genomic windows (both fixed and sliding). 60 Compute variation metrics across genomic windows.
66 61
67 **Examples** 62 **Examples**
68 63
69 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings:: 64 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows::
70 65
71 -w 50000 66 -w 50000
72 -s 0 67 -s 0
73 -t nucl_div 68 -t nucl_div
74 -o mean 69 -o mean
75 70
76 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings:: 71 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb::
77 72
78 -w 50000 73 -w 50000
79 -s 10000 74 -s 10000
80 -t nucl_div 75 -t nucl_div
81 -o mean 76 -o mean
82 77
83 Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings:: 78 Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome::
84 79
85 -w 10000 80 -w 10000
81 -s 100000
86 -t hwe 82 -t hwe
87 -o max 83 -o max
88 84
89 ]]></help> 85 ]]></help>
90 <expand macro="citations"/> 86 <expand macro="citations"/>