Mercurial > repos > iuc > hyphy_absrel

comparison hyphy_absrel.xml @ 26:74c8c33c1b87 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 17:56:01 +0000
parents 81e2754865c9
children c2dffa7ceb65
comparison
equal deleted inserted replaced
25:6548ac548464 26:74c8c33c1b87
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