Mercurial > repos > iuc > hyphy_absrel
comparison hyphy_absrel.xml @ 35:841557158611 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 15:09:44 +0000 |
| parents | 212c958f6cee |
| children |
comparison
equal
deleted
inserted
replaced
| 34:a6619171428e | 35:841557158611 |
|---|---|
| 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 |