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comparison hyphy_absrel.xml @ 0:9e8344d39fb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
author rdvelazquez
date Mon, 10 Sep 2018 12:02:49 -0400
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1 <?xml version="1.0"?>
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
3 <description>: adaptive Branch Site REL</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 ln -s '$input_file' absrel_input.fa &&
12 ln -s '$input_nhx' absrel_input.nhx &&
13 echo $gencodeid > tool_params &&
14 echo `pwd`/absrel_input.fa >> tool_params &&
15 echo `pwd`/absrel_input.nhx >> tool_params &&
16 echo '$branches' >> tool_params &&
17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf > '$absrel_log'
18 ]]>
19 </command>
20 <inputs>
21 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
22 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
23 <param name="gencodeid" type="select" label="Genetic code">
24 <option value="1">Universal code</option>
25 <option value="2">Vertebrate mitochondrial DNA code</option>
26 <option value="3">Yeast mitochondrial DNA code</option>
27 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
28 <option value="5">Invertebrate mitochondrial DNA code</option>
29 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
30 <option value="7">Echinoderm mitochondrial DNA code</option>
31 <option value="8">Euplotid Nuclear code</option>
32 <option value="9">Alternative Yeast Nuclear code</option>
33 <option value="10">Ascidian mitochondrial DNA code</option>
34 <option value="11">Flatworm mitochondrial DNA code</option>
35 <option value="12">Blepharisma Nuclear code</option>
36 </param>
37 <param name="branches" type="select" label="Set of branches to test">
38 <option value="1">All branches</option>
39 <option value="2">Internal branches</option>
40 <option value="3">Leaf branches</option>
41 <option value="4">Unlabeled branches</option>
42 </param>
43 </inputs>
44 <outputs>
45 <data name="absrel_log" format="txt" />
46 <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
47 </outputs>
48 <tests>
49 <test>
50 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
52 <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
53 </test>
54 </tests>
55 <help>
56 <![CDATA[
57 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
58 ]]>
59 </help>
60 <expand macro="citations">
61 <citation type="doi">10.1093/molbev/msv022</citation>
62 </expand>
63 </tool>