genome_diversity: phylogenetic

annotate phylogenetic_tree.xml @ 36:51cd0307fb70

Phylip's extra ouputs are now stored in the job working directory

author	Richard Burhans <burhans@bx.psu.edu>
date	Wed, 20 Nov 2013 16:32:01 -0500
parents	a631c2f6d913
children

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">
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	5 #import json
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	6 #import base64
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	7 #import zlib
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	8 #set $ind_names = $input.dataset.metadata.individual_names
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	9 #set $ind_colms = $input.dataset.metadata.individual_columns
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	12 #set $ind_comp = zlib.compress($ind_json, 9)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	13 #set $ind_arg = base64.b64encode($ind_comp)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	14 phylogenetic_tree.py '$input' '$output' '$output.files_path'
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	15 #if $input_type.choice == '0'
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	16 'gd_snp'
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	17 #if $input_type.data_source.choice == '0'
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	18 'sequence_coverage'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	19 '$input_type.data_source.minimum_coverage'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	20 '$input_type.data_source.minimum_quality'
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	21 #else if $input_type.data_source.choice == '1'
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	22 'estimated_genotype' '0' '0'
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	23 #end if
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	24 #else if $input_type.choice == '1'
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	25 'gd_genotype' 'estimated_genotype' '0' '0'
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	26 #end if
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	27 #if $individuals.choice == '0'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	28 'all_individuals'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	29 #else if $individuals.choice == '1'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	30 '$individuals.p1_input'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	31 #end if
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	32 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	33 'none'
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	34 #else
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	35 '$input.metadata.dbkey'
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	36 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	37 #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	38 #if $draw_tree_options == ''
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	39 ''
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	40 #else
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	41 '-$draw_tree_options'
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	42 #end if
27 8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b Richard Burhans <burhans@bx.psu.edu> parents: 24 diff changeset	43 '$ind_arg'
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	44 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	45
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	46 <inputs>
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	47 <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	48 <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	49 <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	50 <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	51 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	52 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	53 <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	54
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	55 <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	56 <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	57 <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	58 <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	59 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	60 <when value="0">
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_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	62 <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	63 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	64 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	65 <when value="1"/>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	66 </conditional>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	67 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	68 <when value="1">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	69 <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	70 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	71 </conditional>
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	72
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	73 <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	74 <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	75 <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	76 <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	77 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	78 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	79 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	80 <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	81 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	82 </conditional>
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 <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	85 <option value="1" selected="true">Yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	86 <option value="0">No</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	87 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	88
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	89 <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	90 <label>Branch type</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	91 <option value="" selected="true">square</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	92 <option value="d">diagonal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	93 </param>
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 <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	96 <label>Draw branches to scale</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	97 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	98 <option value="s">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	99 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	100
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	101 <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	102 <label>Show branch lengths</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	103 <option value="" selected="true">yes</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	104 <option value="b">no</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	105 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	106
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	107 <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	108 <label>Tree layout</label>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	109 <option value="" selected="true">horizontal</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	110 <option value="v">vertical</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	111 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	112 </inputs>
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 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	115 <data name="output" format="html" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	116 </outputs>
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 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	119 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	120 <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	121 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	122 <param name="minimum_coverage" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	123 <param name="minimum_quality" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	124 <param name="data_source" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	125 <param name="branch_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	126 <param name="scale_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	127 <param name="length_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	128 <param name="layout_style" value="" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	129 <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	130 <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	131 <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	132 <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	133 <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	134 <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	135 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	136 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	137 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	138
31 a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	139 <requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	140 <requirement type="package" version="1.3">phast</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	141 <requirement type="package" version="1.1">quicktree</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	142 <requirement type="package" version="0.1">gd_c_tools</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	143 </requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	144
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3 Richard Burhans <burhans@bx.psu.edu> parents: 27 diff changeset	145
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	146 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	147
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	148 Dataset formats
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	149
24 248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype. Richard Burhans <burhans@bx.psu.edu> parents: 18 diff changeset	150 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	151 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	152 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	153 (`Dataset missing?`_)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	154
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	155 .. _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	156 .. _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	157 .. _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	158 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	159
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	160 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	161
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	162 What it does
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 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	165 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	166 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	167 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	168 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	169 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	170 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	171
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	172 The input parameters are:
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	173
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	174 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	175 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	176
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	177 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	178 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	179 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	180 Specify Individuals tool.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	181
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	182 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	183 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	184 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	185 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	186 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	187 alleles) when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	188
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	189 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	190 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	191 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	192 when estimating their genetic distance.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	193
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	194 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	195 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	196 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	197 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	198 no effect.
14 8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	199
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	200 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	201 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	202 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	203 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	204 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	205 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	206 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	207 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	208 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	209 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	210 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	211 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	212 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	213
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	214 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	215 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	216 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	217 file.
14 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 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	220
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	221 Acknowledgments
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	222
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	223 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	224 QuickTree program from
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	225 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	226
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	227 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	228 http://compgen.bscb.cornell.edu/phast/ .
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	229
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	230 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug] miller-lab parents: diff changeset	231 </tool>

Mercurial > repos > miller-lab > genome_diversity

annotate phylogenetic_tree.xml @ 36:51cd0307fb70