Mercurial > repos > miller-lab > genome_diversity
comparison dpmix.xml @ 21:d6b961721037
Miller Lab Devshed version 4c04e35b18f6
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Mon, 05 Nov 2012 12:44:17 -0500 |
parents | 8ae67e9fb6ff |
children | 248b06e86022 |
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20:8a4b8efbc82c | 21:d6b961721037 |
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8 "$arg" | 8 "$arg" |
9 #end for | 9 #end for |
10 </command> | 10 </command> |
11 | 11 |
12 <inputs> | 12 <inputs> |
13 <param name="input" type="data" format="gd_snp" label="Dataset"> | 13 <param name="input" type="data" format="gd_snp" label="SNP dataset"> |
14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | 14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> |
15 </param> | 15 </param> |
16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> | 16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> |
17 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> | 17 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> |
18 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> | 18 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> |
19 | 19 |
20 <param name="data_source" type="select" format="integer" label="Data source"> | 20 <param name="data_source" type="select" format="integer" label="Similarity metric"> |
21 <option value="0" selected="true">sequence coverage</option> | 21 <option value="0" selected="true">sequence coverage</option> |
22 <option value="1">estimated genotype</option> | 22 <option value="1">estimated genotype</option> |
23 </param> | 23 </param> |
24 | 24 |
25 <param name="switch_penalty" type="integer" min="0" value="10" label="Switch penalty" /> | 25 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> |
26 </inputs> | 26 </inputs> |
27 | 27 |
28 <outputs> | 28 <outputs> |
29 <data name="output" format="tabular" /> | 29 <data name="output" format="tabular" /> |
30 <data name="output2" format="html" /> | 30 <data name="output2" format="html" /> |
69 | 69 |
70 The user specifies two "ancestral" populations (i.e., sources for | 70 The user specifies two "ancestral" populations (i.e., sources for |
71 chromosomes) and a set of potentially admixed individuals, and chooses | 71 chromosomes) and a set of potentially admixed individuals, and chooses |
72 between the sequence coverage or the estimated genotypes to measure | 72 between the sequence coverage or the estimated genotypes to measure |
73 the similarity of genomic intervals in admixed individuals to the two | 73 the similarity of genomic intervals in admixed individuals to the two |
74 classes of ancestral chromosomes. The user also picks a "switch penalty", | 74 classes of ancestral chromosomes. The user also picks a "genotype switch penalty", |
75 typically between 10 and 100. For each potentially admixed individual, | 75 typically between 10 and 100. For each potentially admixed individual, |
76 the program divides the genome into three "genotypes": (0) homozygous | 76 the program divides the genome into three "genotypes": (0) homozygous |
77 for the first ancestral population (i.e., both chromosomes from that | 77 for the first ancestral population (i.e., both chromosomes from that |
78 population), (1) heterozygous, or (2) homozygous for the second ancestral | 78 population), (1) heterozygous, or (2) homozygous for the second ancestral |
79 population. Parts of a chromosome that are labeled as "heterochromatic" | 79 population. Parts of a chromosome that are labeled as "heterochromatic" |
80 are given the non-genotype, 3. Smaller values of the switch penalty | 80 are given the non-genotype "3". Smaller values of the switch penalty |
81 (corresponding to more ancient admixture events) generally lead to the | 81 (corresponding to more ancient admixture events) generally lead to the |
82 reconstruction of more frequent changes between genotypes. | 82 reconstruction of more frequent changes between genotypes. |
83 | 83 |
84 There are two output datasets generated. A tabular dataset with chromosome, | 84 There are two output datasets generated. A tabular dataset with chromosome, |
85 start, stop, and pairs of columns containing the "genotypes" from above | 85 start, stop, and pairs of columns containing the "genotypes" from above |