Mercurial > repos > iuc > hyphy_sm19

comparison hyphy_sm19.xml @ 9:638942ba8e37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
author iuc
date Wed, 22 Apr 2020 12:10:17 -0400
parents 5f1830cb9135
children 2126c9e28ce6
comparison
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8:6cf8d753e93e 9:638942ba8e37
11 #for $n, $partition in enumerate($partitions): 11 #for $n, $partition in enumerate($partitions):
12 '${partition.label}' 12 '${partition.label}'
13 '${partition.regex}' 13 '${partition.regex}'
14 #end for 14 #end for
15 $replicates 15 $replicates
16 --output '$sm19_output'
16 ]]></command> 17 ]]></command>
17 <inputs> 18 <inputs>
18 <param name="input_file" type="data" format="nhx" label="Input tree"/> 19 <param name="input_file" type="data" format="nhx" label="Input tree"/>
19 <repeat name="partitions" min="2" max="50" title="Partitions"> 20 <repeat name="partitions" min="2" max="50" title="Partitions">
20 <param name="label" type="text" label="Partition label"/> 21 <param name="label" type="text" label="Partition label"/>
30 </param> 31 </param>
31 </repeat> 32 </repeat>
32 <param name="replicates" type="integer" min="1" max="1000000" value="100"/> 33 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
33 </inputs> 34 </inputs>
34 <outputs> 35 <outputs>
35 <data name="sm19_output" format="hyphy_results.json" from_work_dir="sm19_input.nhx.json"/> 36 <data name="sm19_output" format="hyphy_results.json" />
36 </outputs> 37 </outputs>
37 <tests> 38 <tests>
38 <test> 39 <test>
39 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/> 40 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
40 <param name="replicates" value="1000"/> 41 <param name="replicates" value="1000"/>
64 </tests> 65 </tests>
65 <help><![CDATA[ 66 <help><![CDATA[
66 67
67 SM2019 : Structured Slatkin-Maddison 68 SM2019 : Structured Slatkin-Maddison
68 ==================================== 69 ====================================
69 70
70 What does this do? 71 What does this do?
71 ------------------ 72 ------------------
72 73
73 Test for evidence of genetically segregated populations, using a "detuned" version of 74 Test for evidence of genetically segregated populations, using a "detuned" version of
74 the Slatkin-Maddison test. 75 the Slatkin-Maddison test.
75 76
76 Brief description 77 Brief description
77 ----------------- 78 -----------------
78 79
106 x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905, 107 x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905,
107 x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e- 108 x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e-
108 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538, 109 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538,
109 x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4. 110 x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4.
110 34574e-06,x_US_x_A_15C:-4.34574e-06); 111 34574e-06,x_US_x_A_15C:-4.34574e-06);
111 112
112 Which can be partitioned into two groups of leaves, those that end in "P", and those that 113 Which can be partitioned into two groups of leaves, those that end in "P", and those that
113 end in "C" 114 end in "C"
114 115
115 1. Reg-exp 1: `P^` 116 1. Reg-exp 1: `P^`
116 2. Reg-exp 2: `C^` 117 2. Reg-exp 2: `C^`
117 118