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comparison gemini_windower.xml @ 0:89783b909302 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:20:44 -0500
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-1:000000000000 0:89783b909302
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Conducting analyses on genome "windows"</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">windower</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 -w $w
14 -s $s
15 -t $window_analysis
16 -o $operation
17 "${ infile }"
18 > "${ outfile }"
19 ]]>
20 </command>
21 <inputs>
22 <expand macro="infile" />
23
24 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
25 <option value="nucl_div">(nucl_div)</option>
26 <option value="hwe">(hwe)</option>
27 </param>
28
29 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
30 <option value="mean">mean</option>
31 <option value="median">median</option>
32 <option value="min">min</option>
33 <option value="max">max</option>
34 <option value="collapse">collapse</option>
35 </param>
36
37 <param name="w" type="integer" value="10000" label="The window size in bp"
38 help="(-w)">
39 <validator type="in_range" min="0"/>
40 </param>
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>
48
49 <outputs>
50 <data name="outfile" format="tabular" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="infile" value="gemini_windower_input.db" ftype="gemini.sqlite" />
55 <param name="w" value="10000" />
56 <param name="window_analysis" value="nucl_div" />
57 <param name="operation" value="mean" />
58 <output name="outfile" file="gemini_windower_result.tabular" />
59 </test>
60 </tests>
61 <help><![CDATA[
62 **What it does**
63
64 It computs variation metrics across genomic windows (both fixed and sliding).
65
66 **Examples**
67
68 Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
69
70 -w 50000
71 -s 0
72 -t nucl_div
73 -o mean
74
75 Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
76
77 -w 50000
78 -s 10000
79 -t nucl_div
80 -o mean
81
82 Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
83
84 -w 10000
85 -t hwe
86 -o max
87
88 ]]></help>
89 <expand macro="citations"/>
90 </tool>