|
0
|
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>
|
