genome_diversity: prepare_population

annotate prepare_population_structure.xml @ 18:f04f40a36cc8

Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.

author	Richard Burhans <burhans@bx.psu.edu>
date	Tue, 23 Oct 2012 12:41:52 -0400
parents	8ae67e9fb6ff
children	248b06e86022

rev	line source
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	2 <description>: Filter and convert to the format needed for these tools</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	4 <command interpreter="python">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	6 #if $individuals.choice == '0'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	7 "all_individuals"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	8 #else if $individuals.choice == '1'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	9 #for $population in $individuals.populations
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	11 "$pop_arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	12 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	13 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	16 "$arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	17 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	18 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	19
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	20 <inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	21 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	22 <conditional name="individuals">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	23 <param name="choice" type="select" label="Individuals">
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	24 <option value="0" selected="true">All individuals</option>
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	25 <option value="1">Specified populations</option>
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	26 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	27 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	28 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	29 <repeat name="populations" title="Population" min="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	30 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	31 </repeat>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	32 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	33 </conditional>
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	36 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	37 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	38
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	39 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	40 <data name="output" format="gd_ped">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	41 <actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	42 <action type="metadata" name="base_name" default="admix" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	43 </actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	44 </data>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	45 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	46
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	47 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	48 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	50 <param name="min_reads" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	51 <param name="min_qual" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	52 <param name="min_spacing" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	53 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	57 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	58 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	59 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	60
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	61 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	62
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	63 Dataset formats
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	64
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	65 The input datasets are in gd_snp_ and gd_indivs_ formats.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	66 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	67
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	68 .. _gd_snp: ./static/formatHelp.html#gd_snp
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	69 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	70 .. _gd_ped: ./static/formatHelp.html#gd_ped
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	71 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	72
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	73 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	74
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	75 What it does
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	76
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	77 This tool converts a gd_snp dataset into the format needed for estimating
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	78 the population structure. You can select the individuals to be included,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	79 by using "population" datasets created via the Specify Individuals tool.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	80 (It is important for these population datasets to have distinguishable names,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	81 since they will be stored in the output's metadata so that subsequent tools
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	82 can use them as labels. If necessary, rename the datasets to give them
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	83 distinct and meaningful names before running this tool.)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	84
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	85 You can also filter the SNPs, based on criteria such as minimum coverage
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	86 (a qualifying SNP must have at least this many reads for every included
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	87 individual), minimum quality score (for every included individual), and/or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	88 minimum spacing (SNPs that are too close together on the same chromosome or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	89 scaffold are discarded). In addition to producing the filtered and formatted
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	90 .map and .ped files for subsequent analysis, the tool reports the number of
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	91 SNPs meeting these conditions, which can be seen by clicking on the eye icon
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	92 in the history panel after the program runs.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	93
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	94 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	95
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	96 Example
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	97
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	98 - input::
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	99
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	100 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	101 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	102 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	103 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	104
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	105 - output cover page::
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	106
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	107 Prepare to look for population structure Galaxy Composite Dataset
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	108 Output completed: 2012-10-01 04:09:36 PM
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	109
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	110 Outputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	111 * admix.ped (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	112 * admix.map (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	113 * Using 222 of 400 SNPs
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	114
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	115 Inputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	116 * Minimum reads covering a SNP, per individual: 6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	117 * Minimum quality value, per individual: 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	118 * Minimum spacing between SNPs on the same scaffold: 0
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	119
18 f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	120 Populations
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	121 * Pop. A
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	122 1. PB1
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	123 2. PB2
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	124 * Pop. B
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	125 1. PB3
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	126 2. PB4
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	127 * Pop. C
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	128 1. PB6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	129 2. PB8
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	130
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	131 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	132 </tool>

Mercurial > repos > miller-lab > genome_diversity

annotate prepare_population_structure.xml @ 18:f04f40a36cc8