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comparison pedverf1stats.xml @ 56:8a06f49972d0 draft

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Added more optional parameters to mabcstats.xml and pedverf1stats.xml
author cropgeeks
date Wed, 15 Nov 2017 06:42:44 -0500
parents 6777844fd638
children 33eaa535ceb4
comparison
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55:6777844fd638 56:8a06f49972d0
6 -Xmx$adv_opts.memory 6 -Xmx$adv_opts.memory
7 #end if 7 #end if
8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats 8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
9 -m $map 9 -m $map
10 -g $genotypes 10 -g $genotypes
11 #if $qtls
12 -q $qtls
13 #end if
14 #if $traits
15 -t $traits
16 #end if
11 -f $parent1 17 -f $parent1
12 -s $parent2 18 -s $parent2
13 -o $output 19 -o $output
14 #if $simulate_f1.simulate_f1_selector == False 20 #if $simulate_f1.simulate_f1_selector == False
15 -e $simulate_f1.expectedF1 21 -e $simulate_f1.expectedF1
30 <param format="fjmap" name="map" type="data" label="Flapjack map file" 36 <param format="fjmap" name="map" type="data" label="Flapjack map file"
31 help="Flapjack-formatted (tab-delimited text) input file of map data"/> 37 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
32 38
33 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" 39 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
34 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> 40 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
41
42 <param format="fjqtl" name="qtls" type="data"
43 label="Flapjack QTL file"
44 help="Flapjack-formatted (tab-delimited text) input file of QTL data."
45 optional="true"/>
46
47 <param format="fjphenotype" name="traits" type="data"
48 label="Flapjack Trait file"
49 help="Flapjack-formatted (tab-delimited text) input file of trait data."
50 optional="true"/>
35 51
36 <param name="parent1" type="integer" value="1" label="Index of parent 1" 52 <param name="parent1" type="integer" value="1" label="Index of parent 1"
37 help="The index of the first parent in the genotype file"/> 53 help="The index of the first parent in the genotype file"/>
38 54
39 <param name="parent2" type="integer" value="2" label="Index of parent 2" 55 <param name="parent2" type="integer" value="2" label="Index of parent 2"