Mercurial > repos > iuc > hyphy_slac

comparison hyphy_slac.xml @ 26:0c6724c345d9 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 18:00:01 +0000
parents ec499ddce7a9
children c010cbc8ff3a
comparison
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25:d430eba4a90e 26:0c6724c345d9
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1" profile="19.09">
3 <description>Single Likelihood Ancestor Counting</description> 3 <description>Single Likelihood Ancestor Counting</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@OPERATION@">SLAC</token>
7 <token name="@operation@">slac</token>
8 </macros> 6 </macros>
9 <expand macro="requirements"/> 7 <expand macro="requirements"/>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 @SYMLINK_FILES@ 9 @SYMLINK_FILES@
12 hyphy slac 10 hyphy slac
13 --alignment ./$input_file 11 --alignment ./$input_file
14 #if $input_nhx: 12 @INPUT_TREE@
15 --tree ./input.nhx
16 #end if
17 --code '$gencodeid' 13 --code '$gencodeid'
18 --branches '$branches' 14 @branch_options@
19 --samples '$number_of_samples' 15 --samples '$number_of_samples'
20 --pvalue '$p_value' 16 --pvalue '$p_value'
21 --output '$slac_output' 17 --output '$slac_output'
22 > '$slac_log' ; 18 @ERRORS@
23 @CATCH_ERROR@
24 ]]></command> 19 ]]></command>
25 <inputs> 20 <inputs>
26 <expand macro="inputs"/> 21 <expand macro="inputs"/>
27 <expand macro="gencode"/> 22 <expand macro="gencode"/>
28 <expand macro="branches"/> 23 <expand macro="branches"/>
29 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> 24 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
30 <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/> 25 <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
31 </inputs> 26 </inputs>
32 <outputs> 27 <outputs>
33 <data name="slac_log" format="txt"/>
34 <data name="slac_output" format="hyphy_results.json" /> 28 <data name="slac_output" format="hyphy_results.json" />
35 </outputs> 29 </outputs>
36 <tests> 30 <tests>
37 <test> 31 <test>
38 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 32 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>