annotate prepare_population_structure.xml @ 7:e29f4d801bb0

change wsf -> snp; wpf -> sap
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 18 Apr 2012 11:12:21 -0400
parents 2c498d40ecde
children 9b92372de9f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
1 <tool id="gd_prepare_population_structure" name="Prepare" version="1.0.0">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
2 <description>to look for population structure</description>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
3
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
4 <command interpreter="python">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
6 #if $individuals.choice == '0'
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
7 "all_individuals"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
8 #else if $individuals.choice == '1'
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
9 #for $population in $individuals.populations
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
11 "$pop_arg"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
12 #end for
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
13 #end if
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
16 "$arg"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
17 #end for
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
18 </command>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
19
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
20 <inputs>
7
e29f4d801bb0 change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents: 0
diff changeset
21 <param name="input" type="data" format="snp" label="SNP table" />
0
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
24 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
25 <conditional name="individuals">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
26 <param name="choice" type="select" label="Individuals">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
27 <option value="0" selected="true">All</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
28 <option value="1">Choose</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
29 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
30 <when value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
31 <when value="1">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
32 <repeat name="populations" title="Population" min="1">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
33 <param name="p_input" type="data" format="ind" label="Individuals" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
34 </repeat>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
35 </when>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
36 </conditional>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
37 </inputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
38
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
39 <outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
40 <data name="output" format="wped">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
41 <actions>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
42 <action type="metadata" name="base_name" default="admix" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
43 </actions>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
44 </data>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
45 </outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
46
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
47 <tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
48 <test>
7
e29f4d801bb0 change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents: 0
diff changeset
49 <param name="input" value="test_in/sample.snp" ftype="snp" />
0
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
50 <param name="min_reads" value="3" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
51 <param name="min_qual" value="30" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
52 <param name="min_spacing" value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
53 <param name="choice" value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
57 </output>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
58 </test>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
59 </tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
60
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
61 <help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
62 **What it does**
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
63
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
64 The tool converts a SNP table into two tables, called "admix.map" and
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
65 "admix.ped", needed for estimating the population structure. The user
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
66 can read or download those files, or simply pass this tool's output on to
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
67 other programs. The user imposes conditions on which SNPs to consider,
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
68 such as the minimum coverage and/or quality value for every individual,
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
69 or the distance to the closest SNP in the same contig (as named in the
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
70 first column of the SNP table). A useful piece of information produced
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
71 by the tool is the number of SNPs meeting those conditions, which can
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
72 be found by clicking on the "eye" after the program runs.
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
73 </help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
74 </tool>