genome_diversity: phylogenetic

annotate phylogenetic_tree.xml @ 21:d6b961721037

Miller Lab Devshed version 4c04e35b18f6

author	Richard Burhans <burhans@bx.psu.edu>
date	Mon, 05 Nov 2012 12:44:17 -0500
parents	f04f40a36cc8
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_phylogenetic_tree" name="Phylogenetic Tree" version="1.0.0">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	2 <description>: Show genetic relationships among individuals</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 phylogenetic_tree.py "$input"
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 $individuals.choice == '1'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	9 "$p1_input"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	10 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	11 "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	12 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	13 "none"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	14 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	15 "$input.metadata.dbkey"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	16 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	17 "$data_source"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	18 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	19 #if $draw_tree_options == ''
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	20 ""
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	21 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	22 "-$draw_tree_options"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	23 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	24 #for $individual_name, $individual_col in zip($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	25 #set $arg = '%s:%s' % ($individual_col, $individual_name)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	26 "$arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	27 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	28 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	29
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	30 <inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	31 <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	32
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	33 <conditional name="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	34 <param name="choice" type="select" label="Compute for">
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	35 <option value="0" selected="true">All individuals</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	36 <option value="1">Individuals in a population</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	37 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	38 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	39 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	40 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	41 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	42 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	43
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 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" />
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	45
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	46 <param name="minimum_quality" 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	47 help="Note: minimum coverage and minimum quality cannot both be 0" />
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	48
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	49 <param name="include_reference" type="select" format="integer" label="Include reference sequence">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	50 <option value="1" selected="true">Yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	51 <option value="0">No</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	52 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	53
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	54 <param name="data_source" type="select" format="integer" label="Distance metric">
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	55 <option value="0" selected="true">sequence coverage</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	56 <option value="1">estimated genotype</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	57 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	58
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	59 <param name="branch_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	60 <label>Branch type</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	61 <option value="" selected="true">square</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	62 <option value="d">diagonal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	63 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	64
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	65 <param name="scale_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	66 <label>Draw branches to scale</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	67 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	68 <option value="s">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	69 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	70
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	71 <param name="length_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	72 <label>Show branch lengths</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	73 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	74 <option value="b">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	75 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	76
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	77 <param name="layout_style" type="select" display="radio">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	78 <label>Tree layout</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	79 <option value="" selected="true">horizontal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	80 <option value="v">vertical</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	81 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	82 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	83
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	84 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	85 <data name="output" format="html" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	86 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	87
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	88 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	89 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	90 <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	91 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	92 <param name="minimum_coverage" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	93 <param name="minimum_quality" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	94 <param name="data_source" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	95 <param name="branch_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	96 <param name="scale_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	97 <param name="length_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	98 <param name="layout_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	99 <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.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	100 <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	101 <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	102 <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	103 <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	104 <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	105 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	106 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	107 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	108
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	109 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	110
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	111 Dataset formats
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	112
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	113 The input dataset is in gd_snp_ format.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	114 The output is a composite dataset, containing the tree in both text (Newick_)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	115 and PostScript formats, as well as supplemental text information.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	116 (`Dataset missing?`_)
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 .. _gd_snp: ./static/formatHelp.html#gd_snp
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	119 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	120 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	121
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	122 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	123
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	124 What it does
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	125
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	126 This tool uses a gd_snp dataset to determine a kind of "genetic distance"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	127 between each pair of individuals. That information is used to
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	128 produce a tree-shaped figure that depicts how the individuals are related,
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	129 both as a text files and as a diagram.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	130 The text files include a common tree format, Newick, as well as distance
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	131 matrices and counts of informative SNPs for each pairwise comparison.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	132 The informative SNPs can be used as a guide to how reliable the tree is.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	133
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	134 The input parameters are:
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	135
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	136 SNP dataset
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	137 A table of SNPs for various individuals, in gd_snp format.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	138
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	139 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	140 By default all individuals are included in the analysis, but this can
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 optionally be restricted to a subset that has been defined using the
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 Specify Individuals tool.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	143
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	144 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	145 For each pair of individuals, the tool looks for informative SNPs, i.e.,
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 where the sequence data for both individuals is adequate. Specifying,
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 say, 7 for this option instructs the tool to consider only SNPs with
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 at least 7 reads in each of the two individuals (regardless of the
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 alleles) when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	150
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	151 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	152 Specifying, say, 37 for this option instructs the tool to consider
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	153 only SNPs with a quality score of at least 37 in both individuals
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	154 when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	155
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	156 Include reference sequence
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	157 For gd_snp datasets containing columns for a reference sequence, the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	158 user can ask that the reference be indicated in the tree, to help with
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	159 rooting it. If the dataset has no reference columns, this option has
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	160 no effect.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	161
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	162 Distance metric
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	163 The genetic distance between two individuals at a given SNP can
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	164 be estimated two ways. One method is to use the absolute value of the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	165 difference in the frequency of the first allele (or equivalently, the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	166 second allele). For instance, if the first individual has 5 reads 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	167 each allele and the second individual has respectively 3 and 6 reads,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	168 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	169 SNP. The other approach is to use the genotype calls to estimate
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	170 the difference in the number of occurrences of the first allele.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	171 For instance, if the two genotypes are 2 and 1, i.e., the individuals
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	172 are estimated to have respectively 2 and 1 occurrences of the first
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	173 allele at this location, then the distance is 1 (the absolute value
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	174 of the difference of the two numbers).
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	175
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	176 Output options
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	177 The final four options apply mostly to the graphical drawing of the
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	178 tree, except that the branch lengths are also added to the Newick text
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools. Richard Burhans <burhans@bx.psu.edu> parents: 14 diff changeset	179 file.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	180
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	181 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	182
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	183 Acknowledgments
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	184
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	185 To convert the distance matrix to a Newick-formatted tree, we use the
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	186 QuickTree program from
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	187 http://www.sanger.ac.uk/resources/software/quicktree/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	188
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	189 To make the diagram we use draw_tree, available at
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	190 http://compgen.bscb.cornell.edu/phast/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	191
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	192 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	193 </tool>

Mercurial > repos > miller-lab > genome_diversity

annotate phylogenetic_tree.xml @ 21:d6b961721037