annotate prepare_population_structure.xml @ 34:f739a296a339

Update to Miller Lab devshed revision 09dc81dbebc5
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 23 Sep 2013 13:37:19 -0400
parents a631c2f6d913
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.2.0">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Filter and convert to the format needed for these tools</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
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 prepare_population_structure.py '$input'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
15 #if $input_type.choice == '0'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
16 'gd_snp' '$input_type.min_reads' '$input_type.min_qual'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
17 #else if $input_type.choice == '1'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
18 'gd_genotype' '0' '0'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
19 #end if
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
20 '0' '$output' '$output.files_path' '$ind_arg'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
21 #if $individuals.choice == '0'
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
22 'all_individuals'
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
23 #else if $individuals.choice == '1'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
24 #for $population in $individuals.populations
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
25 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
26 '$pop_arg'
14
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 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
29 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
30
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
31 <inputs>
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
32 <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
33 <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
34 <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
35 <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
36 </param>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
37 <when value="0">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
38 <param name="input" type="data" format="gd_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
39 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
40 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
41 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
42 <when value="1">
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
43 <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
44 </when>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
45 </conditional>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
46
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
47 <conditional name="individuals">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
48 <param name="choice" type="select" label="Individuals">
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
49 <option value="0" selected="true">All individuals</option>
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
50 <option value="1">Specified populations</option>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
51 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
52 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
53 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
54 <repeat name="populations" title="Population" min="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
55 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
56 </repeat>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
57 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
58 </conditional>
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
59
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
60 <!--
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
61 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
62 "$min_spacing" "$output" "$output.files_path"
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
63 -->
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
64 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
65
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
66 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
67 <data name="output" format="gd_ped">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
68 <actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
69 <action type="metadata" name="base_name" default="admix" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
70 </actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
71 </data>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
72 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
73
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
74 <requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
75 <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
76 </requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
77
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
78 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
79 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
80 <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
81 <param name="min_reads" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
82 <param name="min_qual" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
83 <param name="min_spacing" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
84 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
85 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
86 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
87 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
88 </output>
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 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
91
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
92 <help>
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 **Dataset formats**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
95
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
96 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
97 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
98
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
99 .. _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
100 .. _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
101 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
102 .. _gd_ped: ./static/formatHelp.html#gd_ped
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
103 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
104
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
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
107 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
108
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
109 This tool converts a gd_snp dataset into the format needed for estimating
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
110 the population structure. You can select the individuals to be included,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
111 by using "population" datasets created via the Specify Individuals tool.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
112 (It is important for these population datasets to have distinguishable names,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
113 since they will be stored in the output's metadata so that subsequent tools
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
114 can use them as labels. If necessary, rename the datasets to give them
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
115 distinct and meaningful names before running this tool.)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
116
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
117 You can also filter the SNPs, based on criteria such as minimum coverage
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
118 (a qualifying SNP must have at least this many reads for every included
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
119 individual), minimum quality score (for every included individual), and/or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
120 minimum spacing (SNPs that are too close together on the same chromosome or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
121 scaffold are discarded). In addition to producing the filtered and formatted
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
122 .map and .ped files for subsequent analysis, the tool reports the number of
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
123 SNPs meeting these conditions, which can be seen by clicking on the eye icon
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
124 in the history panel after the program runs.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
125
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
126 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
127
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
128 **Example**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
129
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
130 - input::
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
131
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
132 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
133 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
134 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
135 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
136
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 - output cover page::
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
138
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
139 Prepare to look for population structure Galaxy Composite Dataset
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
140 Output completed: 2012-10-01 04:09:36 PM
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
141
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 Outputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
143 * admix.ped (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
144 * admix.map (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
145 * Using 222 of 400 SNPs
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
146
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
147 Inputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
148 * Minimum reads covering a SNP, per individual: 6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
149 * Minimum quality value, per individual: 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
150 * Minimum spacing between SNPs on the same scaffold: 0
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
151
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
152 Populations
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
153 * Pop. A
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
154 1. PB1
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
155 2. PB2
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
156 * Pop. B
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
157 1. PB3
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
158 2. PB4
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
159 * Pop. C
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
160 1. PB6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
161 2. PB8
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
162
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
163 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
164 </tool>