genome_diversity: phylogenetic

annotate phylogenetic_tree.xml @ 25:cba0d7a63b82

workaround for gd_genotype datatype admix shift int -> float

author	Richard Burhans <burhans@bx.psu.edu>
date	Wed, 29 May 2013 13:49:19 -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_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0">
14 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">
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	5 phylogenetic_tree.py "$input" "$output" "$output.files_path"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	6
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	7 #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	8 "gd_snp"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	9 #if $input_type.data_source.choice == '0'
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	10 "sequence_coverage"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	11 "$input_type.data_source.minimum_coverage"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	12 "$input_type.data_source.minimum_quality"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	13 #else if $input_type.data_source.choice == '1'
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	14 "estimated_genotype"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	15 #end if
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	16 #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	17 "gd_genotype"
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	18 #end if
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	19
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	20 #if $individuals.choice == '0'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	21 "all_individuals"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	22 #else if $individuals.choice == '1'
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	23 "$individuals.p1_input"
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	24 #end if
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	25
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	26 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	27 "none"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	28 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	29 "$input.metadata.dbkey"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	30 #end if
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	31
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	32 #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	33 #if $draw_tree_options == ''
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	34 ""
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	35 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	36 "-$draw_tree_options"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	37 #end if
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	38
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	39 #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	40 #set $arg = '%s:%s' % ($individual_col, $individual_name)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	41 "$arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	42 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	43 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	44
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	45 <inputs>
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	46 <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	47 <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	48 <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	49 <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	50 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	51 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	52 <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	53
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	54 <conditional name="data_source">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	55 <param name="choice" type="select" format="integer" label="Distance metric">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	56 <option value="0">sequence coverage</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	57 <option value="1" selected="true">estimated genotype</option>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	58 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	59 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	60 <param name="minimum_coverage" 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	61 <param name="minimum_quality" 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	62 help="Note: minimum coverage and minimum quality cannot both be 0" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	63 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	64 <when value="1"/>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	65 </conditional>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	66 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	67 <when value="1">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	68 <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	69 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	70 </conditional>
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	71
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	72 <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	73 <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	74 <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	75 <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	76 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	77 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	78 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	79 <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	80 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	81 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	82
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	83 <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	84 <option value="1" selected="true">Yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	85 <option value="0">No</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	86 </param>
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 <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	89 <label>Branch type</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	90 <option value="" selected="true">square</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	91 <option value="d">diagonal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	92 </param>
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 <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	95 <label>Draw branches to scale</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	96 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	97 <option value="s">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	98 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	99
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	100 <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	101 <label>Show branch lengths</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	102 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	103 <option value="b">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	104 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	105
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	106 <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	107 <label>Tree layout</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	108 <option value="" selected="true">horizontal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	109 <option value="v">vertical</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	110 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	111 </inputs>
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 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	114 <data name="output" format="html" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	115 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	116
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	117 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	118 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	119 <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	120 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	121 <param name="minimum_coverage" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	122 <param name="minimum_quality" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	123 <param name="data_source" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	124 <param name="branch_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	125 <param name="scale_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	126 <param name="length_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	127 <param name="layout_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	128 <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	129 <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	130 <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	131 <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	132 <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	133 <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	134 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	135 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	136 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	137
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	138 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	139
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	140 Dataset formats
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	141
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	142 The input dataset is in gd_snp_ or gd_genotype_ format.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	143 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	144 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	145 (`Dataset missing?`_)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	146
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	147 .. _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	148 .. _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	149 .. _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	150 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	151
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	152 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	153
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	154 What it does
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 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	157 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	158 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	159 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	160 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	161 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	162 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	163
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	164 The input parameters are:
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	165
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	166 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	167 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	168
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	169 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	170 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	171 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	172 Specify Individuals tool.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	173
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	174 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	175 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	176 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	177 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	178 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	179 alleles) when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	180
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	181 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	182 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	183 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	184 when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	185
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	186 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	187 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	188 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	189 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	190 no effect.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	191
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	192 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	193 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	194 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	195 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	196 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	197 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	198 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	199 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	200 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	201 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	202 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	203 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	204 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	205
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	206 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	207 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	208 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	209 file.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	210
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	211 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	212
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	213 Acknowledgments
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	214
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	215 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	216 QuickTree program from
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	217 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	218
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	219 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	220 http://compgen.bscb.cornell.edu/phast/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	221
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	222 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	223 </tool>

Mercurial > repos > miller-lab > genome_diversity

annotate phylogenetic_tree.xml @ 25:cba0d7a63b82