Mercurial > repos > iuc > hyphy_absrel
comparison hyphy_absrel.xml @ 26:5f2ca10db92a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author | iuc |
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date | Tue, 27 Apr 2021 18:07:06 +0000 |
parents | 9275e81b5590 |
children | 26de3a7b1cb9 |
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25:f04a1264e2a2 | 26:5f2ca10db92a |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0" profile="19.09"> | 2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1" profile="19.09"> |
3 <description>adaptive Branch Site Random Effects Likelihood</description> | 3 <description>adaptive Branch Site Random Effects Likelihood</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 <token name="@OPERATION@">aBSREL</token> | |
7 <token name="@operation@">absrel</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@ |
10 ln -s '$absrel_output' ${input_file}.aBSREL.json && | |
12 @HYPHYMPI@ absrel | 11 @HYPHYMPI@ absrel |
13 --alignment ./$input_file | 12 --alignment ./$input_file |
14 #if $input_nhx: | 13 @INPUT_TREE@ |
15 --tree ./input.nhx | |
16 #end if | |
17 --code '$gencodeid' | 14 --code '$gencodeid' |
18 --branches '$branches' | 15 @branch_options@ |
19 --output '$absrel_output' | 16 --output '$absrel_output' |
20 --multiple-hits $multiple_hits | 17 --multiple-hits $multiple_hits |
21 #if $log: | 18 @ERRORS@ |
22 > '$absrel_log' | |
23 #end if | |
24 ; | |
25 @CATCH_ERROR@ | |
26 ]]></command> | 19 ]]></command> |
27 <inputs> | 20 <inputs> |
28 <expand macro="inputs"/> | 21 <expand macro="inputs"/> |
29 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> | 22 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> |
30 <expand macro="gencode"/> | 23 <expand macro="gencode"/> |
34 <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> |
35 </param> | 28 </param> |
36 <expand macro="branches"/> | 29 <expand macro="branches"/> |
37 </inputs> | 30 </inputs> |
38 <outputs> | 31 <outputs> |
39 <data name="absrel_log" format="txt"> | |
40 <filter>log</filter> | |
41 </data> | |
42 <data name="absrel_output" format="hyphy_results.json" /> | 32 <data name="absrel_output" format="hyphy_results.json" /> |
43 </outputs> | 33 </outputs> |
44 <tests> | 34 <tests> |
45 <test> | 35 <test> |
46 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> | 36 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
47 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | 37 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
48 <param name="multiple_hits" value="None" /> | 38 <param name="multiple_hits" value="None" /> |
49 <param name="log" value="false"/> | |
50 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> | 39 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> |
51 </test> | 40 </test> |
52 <test> | 41 <test> |
53 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> | 42 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
54 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | 43 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
55 <param name="multiple_hits" value="Double" /> | 44 <param name="multiple_hits" value="Double" /> |
56 <param name="log" value="false"/> | |
57 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> | 45 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> |
58 </test> | 46 </test> |
59 </tests> | 47 </tests> |
60 <help><![CDATA[ | 48 <help><![CDATA[ |
61 | 49 |