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comparison hyphy_absrel.xml @ 35:aa96474b3a87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 14:59:00 +0000
parents 68916eb8887f
children 16093bcfe525
comparison
equal deleted inserted replaced
34:d0e8c77a5302 35:aa96474b3a87
1 <?xml version="1.0"?> 1 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
3 <description>adaptive Branch Site Random Effects Likelihood</description> 2 <description>adaptive Branch Site Random Effects Likelihood</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
20 @ERRORS@ 19 @ERRORS@
21 ]]></command> 20 ]]></command>
22 <inputs> 21 <inputs>
23 <expand macro="inputs"/> 22 <expand macro="inputs"/>
24 <expand macro="gencode"/> 23 <expand macro="gencode"/>
25 <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions"> 24 <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions">
26 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option> 25 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
27 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option> 26 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
28 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option> 27 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
29 </param> 28 </param>
30 <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" /> 29 <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 37 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
39 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
40 <param name="multiple_hits" value="None" /> 39 <param name="multiple_hits" value="None" />
41 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> 40 <output name="absrel_output">
41 <assert_contents>
42 <has_size value="10512" delta="100"/>
43 <has_text text="fits"/>
44 <has_text text="branch attributes"/>
45 <has_text text="Full adaptive model"/>
46 </assert_contents>
47 </output>
48 <assert_stdout>
49 <has_text text="found **2** branches under selection among **5** tested"/>
50 </assert_stdout>
42 </test> 51 </test>
43 <test> 52 <test>
44 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 53 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
45 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 54 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
46 <param name="multiple_hits" value="Double" /> 55 <param name="multiple_hits" value="Double" />
47 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> 56 <output name="absrel_output">
57 <assert_contents>
58 <has_size value="11117" delta="100"/>
59 <has_text text="fits"/>
60 <has_text text="branch attributes"/>
61 <has_text text="Full adaptive model"/>
62 </assert_contents>
63 </output>
64 <assert_stdout>
65 <has_text text="found **0** branches under selection among **5** tested"/>
66 </assert_stdout>
48 </test> 67 </test>
49 <test> 68 <test>
50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 69 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 70 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
52 <param name="multiple_hits" value="Double" /> 71 <param name="multiple_hits" value="Double" />
53 <param name="srv" value="--srv Yes" /> 72 <param name="srv" value="true" />
54 <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/> 73 <output name="absrel_output">
74 <assert_contents>
75 <has_size value="23396" delta="100"/>
76 <has_text text="fits"/>
77 <has_text text="branch attributes"/>
78 <has_text text="Full adaptive model"/>
79 </assert_contents>
80 </output>
81 <assert_stdout>
82 <has_text text="found **0** branches under selection among **5** tested"/>
83 </assert_stdout>
55 </test> 84 </test>
56 </tests> 85 </tests>
57 <help><![CDATA[ 86 <help><![CDATA[
58 87
59 aBSREL : Adaptive Branch-Site Random Effects Likelihood 88 aBSREL : Adaptive Branch-Site Random Effects Likelihood