Mercurial > repos > miller-lab > genome_diversity
diff 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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--- a/dpmix.xml Tue Oct 23 14:38:04 2012 -0400 +++ b/dpmix.xml Mon Nov 05 12:44:17 2012 -0500 @@ -10,19 +10,19 @@ </command> <inputs> - <param name="input" type="data" format="gd_snp" label="Dataset"> + <param name="input" type="data" format="gd_snp" label="SNP dataset"> <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> </param> <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> - <param name="data_source" type="select" format="integer" label="Data source"> + <param name="data_source" type="select" format="integer" label="Similarity metric"> <option value="0" selected="true">sequence coverage</option> <option value="1">estimated genotype</option> </param> - <param name="switch_penalty" type="integer" min="0" value="10" label="Switch penalty" /> + <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> </inputs> <outputs> @@ -71,13 +71,13 @@ chromosomes) and a set of potentially admixed individuals, and chooses between the sequence coverage or the estimated genotypes to measure the similarity of genomic intervals in admixed individuals to the two -classes of ancestral chromosomes. The user also picks a "switch penalty", +classes of ancestral chromosomes. The user also picks a "genotype switch penalty", typically between 10 and 100. For each potentially admixed individual, the program divides the genome into three "genotypes": (0) homozygous for the first ancestral population (i.e., both chromosomes from that population), (1) heterozygous, or (2) homozygous for the second ancestral population. Parts of a chromosome that are labeled as "heterochromatic" -are given the non-genotype, 3. Smaller values of the switch penalty +are given the non-genotype "3". Smaller values of the switch penalty (corresponding to more ancient admixture events) generally lead to the reconstruction of more frequent changes between genotypes.