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comparison gemini_windower.xml @ 0:14caa57eca63 draft

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author iuc
date Mon, 11 Aug 2014 07:44:30 -0400
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-1:000000000000 0:14caa57eca63
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Conducting analyses on genome "windows"</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">windower</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini @BINARY@
12 -w $w
13 -s $s
14 -t $window_analysis
15 -o $operation
16 "${ infile }"
17 > "${ outfile }"
18 ]]>
19 </command>
20 <expand macro="stdio" />
21 <inputs>
22 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
23
24 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
25 <option value="nucl_div">(nucl_div)</option>
26 <option value="hwe">(hwe)</option>
27 </param>
28
29 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
30 <option value="mean">mean</option>
31 <option value="median">median</option>
32 <option value="min">min</option>
33 <option value="max">max</option>
34 <option value="collapse">collapse</option>
35 </param>
36
37 <param name="w" type="integer" value="10000" size="10" label="The window size in bp"
38 help="(-w)">
39 <validator type="in_range" min="0"/>
40 </param>
41
42 <param name="s" type="integer" value="1000" size="10" label="The step size for the windows in bp"
43 help="(-s)">
44 <validator type="in_range" min="0"/>
45 </param>
46
47 </inputs>
48
49 <outputs>
50 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
51 </outputs>
52 <tests>
53 <test>
54 </test>
55 </tests>
56 <help>
57 **What it does**
58
59 It computs variation metrics across genomic windows (both fixed and sliding).
60
61 @CITATION@
62 </help>
63 <expand macro="citations"/>
64 </tool>