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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
author iuc
date Fri, 17 Mar 2017 15:20:38 -0400
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1 <tool id="BayeScan" name="BayeScan" version="2.1">
2 <description>Detecting natural selection from population-based genetic data</description>
3 <requirements>
4 <requirement type="package" version="2.0.1">bayescan</requirement>
5 </requirements>
6 <command>
7
8 <![CDATA[
9 mkdir 'output_dir';
10
11 bayescan2 '$input'
12 -od output_dir
13 #if '$loci_file.loci' == "1"
14 -d '$loci_file.input_loci'
15 #end if
16 '$snp_genotypes_matrix'
17 '$fstats'
18 '$pilot_runs'
19 '$allele_frequency'
20 -o bayescan
21 -n '$sample_size'
22 -thin '$thinning_interval'
23 -nbp '$num_pilot_runs'
24 -pilot '$length_pilot_run'
25 -burn '$burn'
26 -pr_odds '$prior_odds'
27 -lb_fis '$lower_prior'
28 -hb_fis '$higher_prior'
29 -aflp_pc '$threshold' > '$output'
30 ]]>
31
32 </command>
33
34 <inputs>
35
36 <param name="input" type="data" format="tabular,txt" label="Input genotype data file" help="must be space/tab delimitted plain text file" />
37 <conditional name="loci_file">
38 <param name="loci" type="select" label="Discard loci?" help="" >
39 <option value="0">No</option>
40 <option value="1">Yes</option>
41 </param>
42 <when value="0"></when>
43 <when value="1">
44 <param name="input_loci" type="data" format="tabular,txt" label="Discard loci file" help="Optional input file containing list of loci to discard" />
45 </when>
46 </conditional>
47 <param name="snp_genotypes_matrix" type="boolean" checked="false" truevalue="-fstat" falsevalue="" label="SNP genotypes matrix data" help="Use SNP genotypes matrix"/>
48
49 <param name="fstats" type="boolean" checked="false" truevalue="-snp" falsevalue="" label="Only estimate F-stats (no selection)"/>
50
51 <param name="sample_size" type="integer" value="5000" label="Number of outputted iterations"/>
52 <param name="thinning_interval" type="integer" value="10" label="Thinning interval size"/>
53 <param name="num_pilot_runs" type="integer" value="20" label="Number of pilot runs" />
54 <param name="length_pilot_run" type="integer" value="5000" label="Length of pilot runs" />
55 <param name="burn" type="integer" value="50000" label="Additional burn-in length" help="Nlength of an interval between two draws in MCMC"/>
56
57 <param name="prior_odds" type="integer" value="10" size="3" label="Prior odds for the neutral model"/>
58 <param name="lower_prior" type="float" value="0.0" label="Lower bound for uniform prior on Fis (dominant data)"/>
59 <param name="higher_prior" type="float" value="1.0" label="Higher bound for uniform prior on Fis (dominant data)"/>
60 <param name="threshold" type="float" value="0.1" label="Threshold for the recessive genotype as a fraction of maximum band intensity"/>
61
62 <param name="pilot_runs" type="boolean" checked="false" truevalue="-out_pilot" falsevalue="" label="Optional output file for pilot runs"/>
63 <param name="allele_frequency" type="boolean" checked="false" truevalue="-out_freq" falsevalue="" label="Optional output file for allele frequencies"/>
64
65
66 </inputs>
67
68 <outputs>
69 <data format="txt" name="output">
70 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
71 </data>
72 </outputs>
73
74 <tests>
75 <test>
76 <param name="input" value="test_binary_AFLP.txt" />
77 <param name="loci" value="0" />
78 <param name="snp_genotypes_matrix" value="true" />
79 <param name="fstats" value="true"/>
80
81 <param name="sample_size" value="5000" />
82 <param name="thinning_interval" value="10" />
83 <param name="num_pilot_runs" value="20" />
84 <param name="length_pilot_run" value="5000" />
85 <param name="burn" value="50000" />
86
87 <param name="prior_odds" value="10"/>
88 <param name="lower_prior" value="0.0" />
89 <param name="higher_prior" value="1.0"/>
90 <param name="threshold" value="0.1"/>
91
92 <param name="pilot_runs" value="true"/>
93 <param name="allele_frequency" value="true" />
94
95 <output name="output" file="result.out" ftype="txt">
96 <discovered_dataset designation="bayescan" ftype="sel">
97 <assert_contents>
98 <has_text text="logL Fis1 Fis2 Fis3 Fis4 Fis5 Fis6 Fis7 Fis8 Fis9 Fis10 Fst1 Fst2 Fst3 Fst4 Fst5 Fst6 Fst7 Fst8 Fst9 Fst10" />
99 </assert_contents>
100 </discovered_dataset>
101 <discovered_dataset designation="bayescan_Verif" ftype="txt" value="verif.txt" />
102 <discovered_dataset designation="bayescan_AccRte" ftype="txt">
103 <assert_contents>
104 <has_line_matching expression="alpha beta ances freq a_p.*" />
105 </assert_contents>
106 </discovered_dataset>
107 <discovered_dataset designation="bayescan_prop" ftype="txt" value="pilot.txt" />
108 <discovered_dataset designation="bayescan_freq" ftype="txt">
109 <assert_contents>
110 <has_text text="locus1 locus2 locus3 locus4 locus5 locus6 locus7 locus8 locus9 locus10" />
111 </assert_contents>
112 </discovered_dataset>
113 </output>
114 </test>
115 </tests>
116
117 <help><![CDATA[
118
119 **What it does**
120
121 This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
122
123 `BayeScan`_ is based on the multinomial-Dirichlet model.
124
125 One of the simplest possible scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient.
126
127 Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.
128
129 .. _Bayescan: http://cmpg.unibe.ch/software/BayeScan/
130
131 .. class:: infomark
132
133 **Input file**
134
135 BayeScan uses its own input file formats, which depend on the type of data used. All input files are simply in text format.
136
137 Read the `manual`_ to create the input file.
138
139 .. _manual: http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf
140
141 ]]>
142
143 </help>
144 <citations>
145 <citation type="doi">10.1534/genetics.108.092221</citation>
146 </citations>
147 </tool>