Mercurial > repos > iuc > hyphy_absrel

comparison hyphy_absrel.xml @ 33:68916eb8887f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Tue, 29 Mar 2022 23:56:32 +0000
parents 616fb1677838
children aa96474b3a87
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32:616fb1677838 33:68916eb8887f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09"> 2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
3 <description>adaptive Branch Site Random Effects Likelihood</description> 3 <description>adaptive Branch Site Random Effects Likelihood</description>
4 <expand macro="bio_tools"/>
5 <macros> 4 <macros>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @SYMLINK_FILES@ 10 @SYMLINK_FILES@
11 ln -s '$absrel_output' ${input_file}.aBSREL.json && 11 ln -s '$absrel_output' ${input_file}.aBSREL.json &&
12 @HYPHYMPI@ absrel 12 @HYPHYMPI@ absrel
14 @INPUT_TREE@ 14 @INPUT_TREE@
15 --code '$gencodeid' 15 --code '$gencodeid'
16 @branch_options@ 16 @branch_options@
17 --output '$absrel_output' 17 --output '$absrel_output'
18 --multiple-hits $multiple_hits 18 --multiple-hits $multiple_hits
19 $srv
19 @ERRORS@ 20 @ERRORS@
20 ]]></command> 21 ]]></command>
21 <inputs> 22 <inputs>
22 <expand macro="inputs"/> 23 <expand macro="inputs"/>
23 <expand macro="gencode"/> 24 <expand macro="gencode"/>
24 <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions"> 25 <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
25 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option> 26 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
26 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option> 27 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
27 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option> 28 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
28 </param> 29 </param>
30 <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
29 <expand macro="branches"/> 31 <expand macro="branches"/>
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data name="absrel_output" format="hyphy_results.json" /> 34 <data name="absrel_output" format="hyphy_results.json" />
33 </outputs> 35 </outputs>
41 <test> 43 <test>
42 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 44 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
43 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 45 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
44 <param name="multiple_hits" value="Double" /> 46 <param name="multiple_hits" value="Double" />
45 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> 47 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
48 </test>
49 <test>
50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
52 <param name="multiple_hits" value="Double" />
53 <param name="srv" value="--srv Yes" />
54 <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/>
46 </test> 55 </test>
47 </tests> 56 </tests>
48 <help><![CDATA[ 57 <help><![CDATA[
49 58
50 aBSREL : Adaptive Branch-Site Random Effects Likelihood 59 aBSREL : Adaptive Branch-Site Random Effects Likelihood