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comparison hyphy_relax.xml @ 0:551616a65f8f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:24:55 -0400
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children 1da578d6a253
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-1:000000000000 0:551616a65f8f
1 <?xml version="1.0"?>
2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
3 <description>Detect relaxed selection in a codon-based
4 phylogenetic framework</description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_file' relax_input.fa &&
11 ln -s '$input_nhx' relax_input.nhx &&
12 @HYPHY_INVOCATION@ relax
13 --alignment ./relax_input.fa
14 --tree ./relax_input.nhx
15 --models '$analysisType'
16 #if $treeAnnotations == "2":
17 --test TEST
18 --reference REFERENCE
19 #else:
20 --test TEST
21 #end if
22 > '$relax_log'
23 ]]></command>
24 <inputs>
25 <expand macro="inputs"/>
26 <expand macro="gencode"/>
27 <param name="analysisType" type="select" label="Analysis Type">
28 <option value="All">All</option>
29 <option value="Minimal">Minimal</option>
30 </param>
31 <param name="treeAnnotations" type="select" label="Tree Annotations">
32 <option value="1">TEST only</option>
33 <option value="2">TEST and REFERENCE</option>
34 </param>
35 </inputs>
36 <outputs>
37 <data name="relax_log" format="txt"/>
38 <data name="relax_output" format="hyphy_results.json" from_work_dir="relax_input.fa.RELAX.json"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
43 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
44 <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
45 </test>
46 </tests>
47 <help><![CDATA[
48 RELAX (Detect relaxed selection in a codon-based phylogenetic framework)
49 ]]></help>
50 <expand macro="citations">
51 <citation type="doi">10.1093/molbev/msu400</citation>
52 </expand>
53 </tool>