diff dpmix.xml @ 21:d6b961721037

Miller Lab Devshed version 4c04e35b18f6

--- 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.