Mercurial > repos > iuc > hyphy_prime

comparison hyphy_prime.xml @ 17:6d29207a32c5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:04:23 +0000
parents 296f6bc03fa6
children b044a346c00d
comparison
equal deleted inserted replaced
16:a61b2b6c7089 17:6d29207a32c5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy1" profile="19.09">
3 <description>Property Informed Models of Evolution</description> 3 <description>Property Informed Models of Evolution</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@OPERATION@">PRIME</token>
7 <token name="@operation@">prime</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 @HYPHYMPI@ prime 10 @HYPHYMPI@ prime
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 --pvalue '$p_value' 15 --pvalue '$p_value'
20 --properties '$prop_set' 16 --properties '$prop_set'
17 --impute-states '$impute_states'
21 --output '$prime_output' 18 --output '$prime_output'
22 > '$prime_log' 19 @ERRORS@
23 ;
24 @CATCH_ERROR@
25 ]]></command> 20 ]]></command>
26 <inputs> 21 <inputs>
27 <expand macro="inputs"/> 22 <expand macro="inputs"/>
28 <expand macro="gencode"/> 23 <expand macro="gencode"/>
29 <expand macro="branches"/> 24 <expand macro="branches"/>
30 <param name="prop_set" type="select" label="Biochemical properties to use"> 25 <param name="prop_set" type="select" label="Biochemical properties to use">
31 <option value="Atchley">Atchley</option> 26 <option value="Atchley">Atchley</option>
32 <option value="LCAP">LCAP</option> 27 <option value="LCAP">LCAP</option>
33 </param> 28 </param>
34 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> 29 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
30 <param argument="--impute-states" type="boolean" truevalue="Yes" falsevalue="No" label="Use site-level model fits to impute likely character states for each sequence"/>
35 </inputs> 31 </inputs>
36 <outputs> 32 <outputs>
37 <data name="prime_log" format="txt"/>
38 <data name="prime_output" format="hyphy_results.json" /> 33 <data name="prime_output" format="hyphy_results.json" />
39 </outputs> 34 </outputs>
40 <tests> 35 <tests>
41 <test> 36 <test>
42 <param name="input_file" ftype="fasta" value="prime-in1.fa"/> 37 <param name="input_file" ftype="fasta" value="prime-in1.fa"/>