genome_diversity: prepare_population

annotate prepare_population_structure.xml @ 26:91e835060ad2

Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype

author	Richard Burhans <burhans@bx.psu.edu>
date	Mon, 03 Jun 2013 12:29:29 -0400
parents	248b06e86022
children	8997f2ca8c7a

rev	line source
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.1.0">
14 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">
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	5 prepare_population_structure.py "$input"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	6 #if $input_type.choice == '0'
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	7 "gd_snp" "$input_type.min_reads" "$input_type.min_qual"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	8 #else if $input_type.choice == '1'
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	9 "gd_genotype" "0" "0"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	10 #end if
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	11 "$min_spacing" "$output" "$output.files_path"
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	12 #if $individuals.choice == '0'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	13 "all_individuals"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	14 #else if $individuals.choice == '1'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	15 #for $population in $individuals.populations
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	16 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	17 "$pop_arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	18 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	19 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	20 #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	21 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	22 "$arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	23 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	24 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	25
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	26 <inputs>
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	27 <conditional name="input_type">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	28 <param name="choice" type="select" format="integer" label="Input format">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	29 <option value="0" selected="true">gd_snp</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	30 <option value="1">gd_genotype</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	31 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	32 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	33 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	36 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	37 <when value="1">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	38 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	39 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	40 </conditional>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	41
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	42 <conditional name="individuals">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	43 <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	44 <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	45 <option value="1">Specified populations</option>
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	46 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	47 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	48 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	49 <repeat name="populations" title="Population" min="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	50 <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	51 </repeat>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	52 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	53 </conditional>
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	54
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	55 <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	56 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	57
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	58 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	59 <data name="output" format="gd_ped">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	60 <actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	61 <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	62 </actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	63 </data>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	64 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	65
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	66 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	67 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	68 <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	69 <param name="min_reads" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	70 <param name="min_qual" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	71 <param name="min_spacing" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	72 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	73 <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	74 <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	75 <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	76 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	77 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	78 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	79
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	80 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	81
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	82 Dataset formats
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	83
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	84 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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	85 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	86
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	87 .. _gd_snp: ./static/formatHelp.html#gd_snp
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	88 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	89 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	90 .. _gd_ped: ./static/formatHelp.html#gd_ped
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	91 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	92
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 What it does
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	96
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	97 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	98 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	99 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	100 (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	101 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	102 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	103 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	104
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 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	106 (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	107 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	108 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	109 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	110 .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	111 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	112 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	113
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	114 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	115
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	116 Example
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	117
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	118 - input::
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 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	121 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	122 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	123 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	124
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	125 - 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	126
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 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	128 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	129
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	130 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	131 * 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	132 * 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	133 * Using 222 of 400 SNPs
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	134
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	135 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	136 * 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	137 * 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	138 * 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	139
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	140 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	141 * 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	142 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	143 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	144 * 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	145 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	146 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	147 * 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	148 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	149 2. PB8
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	150
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	151 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	152 </tool>

Mercurial > repos > miller-lab > genome_diversity

annotate prepare_population_structure.xml @ 26:91e835060ad2