Mercurial > repos > iuc > hyphy_fade

comparison hyphy_fade.xml @ 25:8b682ac0921b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 17:55:16 +0000
parents 953a2c000bd4
children 491e16494d87
comparison
equal deleted inserted replaced
24:2e7676c24e2e 25:8b682ac0921b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1" profile="19.09">
3 <description>: FUBAR* Approach to Directional Evolution (*Fast 3 <description>: FUBAR* Approach to Directional Evolution (*Fast
4 Unconstrained Bayesian Approximation)</description> 4 Unconstrained Bayesian Approximation)</description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <token name="@OPERATION@">FADE</token>
8 <token name="@operation@">fade</token>
9 </macros> 7 </macros>
10 <expand macro="requirements"/> 8 <expand macro="requirements"/>
11 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
12 @SYMLINK_FILES@ 10 @SYMLINK_FILES@
13 hyphy fade 11 hyphy fade
14 --alignment ./$input_file 12 --alignment $input_file
15 #if $input_nhx: 13 @INPUT_TREE@
16 --tree ./input.nhx 14 @branch_options@
17 #end if
18 --branches '$branches'
19 --model '$model' 15 --model '$model'
20 --method '$posteriorEstimationMethod.method' 16 --method '$posteriorEstimationMethod.method'
21 --grid '$grid_points' 17 --grid '$grid_points'
22 --concentration_parameter '$concentration' 18 --concentration_parameter '$concentration'
23 @posteriorEstimationMethod_cmd@ 19 @posteriorEstimationMethod_cmd@
24 --output '$fade_output' 20 --output '$fade_output'
25 > '$fade_log' ; 21 @ERRORS@
26 @CATCH_ERROR@
27 ]]></command> 22 ]]></command>
28 <inputs> 23 <inputs>
29 <expand macro="inputs"/> 24 <expand macro="inputs"/>
30 <expand macro="branches"/> 25 <expand macro="branches"/>
31 <expand macro="substitution"/> 26 <expand macro="substitution"/>
33 <expand macro="conditional_posteriorEstimationMethod" /> 28 <expand macro="conditional_posteriorEstimationMethod" />
34 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> 29 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
35 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> 30 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
36 </inputs> 31 </inputs>
37 <outputs> 32 <outputs>
38 <data name="fade_log" format="txt"/>
39 <data name="fade_output" format="hyphy_results.json" /> 33 <data name="fade_output" format="hyphy_results.json" />
40 </outputs> 34 </outputs>
41 <tests> 35 <tests>
42 <test> 36 <test>
43 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> 37 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>