Mercurial > repos > iuc > gemini_windower
comparison gemini_windower.xml @ 5:3b5b1ebc8423 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author | iuc |
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date | Fri, 11 Jan 2019 17:38:04 -0500 |
parents | 9aad9ef0502c |
children | 406d3552beca |
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4:9aad9ef0502c | 5:3b5b1ebc8423 |
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> | 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"/> |