Mercurial > repos > iuc > bayescan

annotate bayescan.xml @ 1:d8517994d64e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Mon, 30 Aug 2021 21:46:35 +0000
parents 931d7514a5eb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
1 <tool id="BayeScan" name="BayeScan" version="2.1">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
2 <description>Detecting natural selection from population-based genetic data</description>
1
d8517994d64e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
3 <xrefs>
d8517994d64e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
4 <xref type="bio.tools">bayescan</xref>
d8517994d64e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
5 </xrefs>
0
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
6 <requirements>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
7 <requirement type="package" version="2.0.1">bayescan</requirement>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
8 </requirements>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
9 <command>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
10
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
11 <![CDATA[
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
12 mkdir 'output_dir';
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
13
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
14 bayescan2 '$input'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
15 -od output_dir
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
16 #if '$loci_file.loci' == "1"
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
17 -d '$loci_file.input_loci'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
18 #end if
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
19 '$snp_genotypes_matrix'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
20 '$fstats'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
21 '$pilot_runs'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
22 '$allele_frequency'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
23 -o bayescan
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
24 -n '$sample_size'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
25 -thin '$thinning_interval'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
26 -nbp '$num_pilot_runs'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
27 -pilot '$length_pilot_run'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
28 -burn '$burn'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
29 -pr_odds '$prior_odds'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
30 -lb_fis '$lower_prior'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
31 -hb_fis '$higher_prior'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
32 -aflp_pc '$threshold' > '$output'
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
33 ]]>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
34
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
35 </command>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
36
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
37 <inputs>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
38
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
39 <param name="input" type="data" format="tabular,txt" label="Input genotype data file" help="must be space/tab delimitted plain text file" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
40 <conditional name="loci_file">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
41 <param name="loci" type="select" label="Discard loci?" help="" >
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
42 <option value="0">No</option>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
43 <option value="1">Yes</option>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
44 </param>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
45 <when value="0"></when>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
46 <when value="1">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
47 <param name="input_loci" type="data" format="tabular,txt" label="Discard loci file" help="Optional input file containing list of loci to discard" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
48 </when>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
49 </conditional>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
50 <param name="snp_genotypes_matrix" type="boolean" checked="false" truevalue="-fstat" falsevalue="" label="SNP genotypes matrix data" help="Use SNP genotypes matrix"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
51
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
52 <param name="fstats" type="boolean" checked="false" truevalue="-snp" falsevalue="" label="Only estimate F-stats (no selection)"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
53
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
54 <param name="sample_size" type="integer" value="5000" label="Number of outputted iterations"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
55 <param name="thinning_interval" type="integer" value="10" label="Thinning interval size"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
56 <param name="num_pilot_runs" type="integer" value="20" label="Number of pilot runs" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
57 <param name="length_pilot_run" type="integer" value="5000" label="Length of pilot runs" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
58 <param name="burn" type="integer" value="50000" label="Additional burn-in length" help="Nlength of an interval between two draws in MCMC"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
59
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
60 <param name="prior_odds" type="integer" value="10" size="3" label="Prior odds for the neutral model"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
61 <param name="lower_prior" type="float" value="0.0" label="Lower bound for uniform prior on Fis (dominant data)"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
62 <param name="higher_prior" type="float" value="1.0" label="Higher bound for uniform prior on Fis (dominant data)"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
63 <param name="threshold" type="float" value="0.1" label="Threshold for the recessive genotype as a fraction of maximum band intensity"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
64
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
65 <param name="pilot_runs" type="boolean" checked="false" truevalue="-out_pilot" falsevalue="" label="Optional output file for pilot runs"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
66 <param name="allele_frequency" type="boolean" checked="false" truevalue="-out_freq" falsevalue="" label="Optional output file for allele frequencies"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
67
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
68
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
69 </inputs>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
70
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
71 <outputs>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
72 <data format="txt" name="output">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
73 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
74 </data>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
75 </outputs>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
76
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
77 <tests>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
78 <test>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
79 <param name="input" value="test_binary_AFLP.txt" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
80 <param name="loci" value="0" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
81 <param name="snp_genotypes_matrix" value="true" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
82 <param name="fstats" value="true"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
83
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
84 <param name="sample_size" value="5000" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
85 <param name="thinning_interval" value="10" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
86 <param name="num_pilot_runs" value="20" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
87 <param name="length_pilot_run" value="5000" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
88 <param name="burn" value="50000" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
89
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
90 <param name="prior_odds" value="10"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
91 <param name="lower_prior" value="0.0" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
92 <param name="higher_prior" value="1.0"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
93 <param name="threshold" value="0.1"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
94
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
95 <param name="pilot_runs" value="true"/>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
96 <param name="allele_frequency" value="true" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
97
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
98 <output name="output" file="result.out" ftype="txt">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
99 <discovered_dataset designation="bayescan" ftype="sel">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
100 <assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
101 <has_text text="logL Fis1 Fis2 Fis3 Fis4 Fis5 Fis6 Fis7 Fis8 Fis9 Fis10 Fst1 Fst2 Fst3 Fst4 Fst5 Fst6 Fst7 Fst8 Fst9 Fst10" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
102 </assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
103 </discovered_dataset>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
104 <discovered_dataset designation="bayescan_Verif" ftype="txt" value="verif.txt" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
105 <discovered_dataset designation="bayescan_AccRte" ftype="txt">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
106 <assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
107 <has_line_matching expression="alpha beta ances freq a_p.*" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
108 </assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
109 </discovered_dataset>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
110 <discovered_dataset designation="bayescan_prop" ftype="txt" value="pilot.txt" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
111 <discovered_dataset designation="bayescan_freq" ftype="txt">
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
112 <assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
113 <has_text text="locus1 locus2 locus3 locus4 locus5 locus6 locus7 locus8 locus9 locus10" />
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
114 </assert_contents>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
115 </discovered_dataset>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
116 </output>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
117 </test>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
118 </tests>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
119
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
120 <help><![CDATA[
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
121
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
122 **What it does**
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
123
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
124 This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
125
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
126 `BayeScan`_ is based on the multinomial-Dirichlet model.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
127
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
128 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.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
129
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
130 Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
131
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
132 .. _Bayescan: http://cmpg.unibe.ch/software/BayeScan/
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
133
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
134 .. class:: infomark
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
135
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
136 **Input file**
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
137
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
138 BayeScan uses its own input file formats, which depend on the type of data used. All input files are simply in text format.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
139
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
140 Read the `manual`_ to create the input file.
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
141
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
142 .. _manual: http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
143
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
144 ]]>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
145
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
146 </help>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
147 <citations>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
148 <citation type="doi">10.1534/genetics.108.092221</citation>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
149 </citations>
931d7514a5eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ commit 33637968e1e32c02d7765a6701e930a0ea0dd903
iuc
parents:
diff changeset
150 </tool>