Mercurial > repos > iuc > hyphy_fade

comparison hyphy_fade.xml @ 23:17ac281a46d9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:25:54 +0000
parents 7dbcce65a8ff
children 5e8d0e777033
comparison
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22:c6355a5b0483 23:17ac281a46d9
2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0" 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>
7 </macros> 9 </macros>
8 <expand macro="requirements"/> 10 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_file' fade_input.fa && 12 @SYMLINK_FILES@
11 ln -s '$input_nhx' fade_input.nhx &&
12 hyphy fade 13 hyphy fade
13 --alignment ./fade_input.fa 14 --alignment ./$input_file
14 --tree ./fade_input.nhx 15 #if $input_nhx:
16 --tree ./input.nhx
17 #end if
15 --branches '$branches' 18 --branches '$branches'
16 --model '$model' 19 --model '$model'
17 --method '$posteriorEstimationMethod.method' 20 --method '$posteriorEstimationMethod.method'
18 --grid '$grid_points' 21 --grid '$grid_points'
19 --concentration_parameter '$concentration' 22 --concentration_parameter '$concentration'
20 @posteriorEstimationMethod_cmd@ 23 @posteriorEstimationMethod_cmd@
21 --output '$fade_output' 24 --output '$fade_output'
22 > '$fade_log' 25 > '$fade_log' ;
26 @CATCH_ERROR@
23 ]]></command> 27 ]]></command>
24 <inputs> 28 <inputs>
25 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/> 29 <expand macro="inputs"/>
26 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
27 <expand macro="branches"/> 30 <expand macro="branches"/>
28 <expand macro="substitution"/> 31 <expand macro="substitution"/>
29 <expand macro="branches"/> 32 <expand macro="branches"/>
30 <expand macro="conditional_posteriorEstimationMethod" /> 33 <expand macro="conditional_posteriorEstimationMethod" />
31 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> 34 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>