Mercurial > repos > iuc > hyphy_fel
comparison hyphy_fel.xml @ 0:24a2bf70dbdd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author | iuc |
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date | Thu, 17 Jan 2019 04:23:36 -0500 |
parents | |
children | 6c3ece5fb602 |
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-1:000000000000 | 0:24a2bf70dbdd |
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1 <?xml version="1.0"?> | |
2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> | |
3 <description>Fixed Effects Likelihood</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <expand macro="version_command" /> | |
9 <command detect_errors="exit_code"> | |
10 <![CDATA[ | |
11 ln -s '$input_file' fel_input.fa && | |
12 ln -s '$input_nhx' fel_input.nhx && | |
13 echo $gencodeid > tool_params && | |
14 echo `pwd`/fel_input.fa >> tool_params && | |
15 echo `pwd`/fel_input.nhx >> tool_params && | |
16 echo '$branches' >> tool_params && | |
17 echo '$include_srv' >> tool_params && | |
18 echo '$p_value' >> tool_params && | |
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$fel_log' | |
20 ]]> | |
21 </command> | |
22 <inputs> | |
23 <expand macro="inputs" /> | |
24 <expand macro="gencode" /> | |
25 <expand macro="branches" /> | |
26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> | |
27 <param name="include_srv" type="select" label="Include synonymous rate variation"> | |
28 <option value="1">Yes (recommended)</option> | |
29 <option value="2">No</option> | |
30 </param> | |
31 </inputs> | |
32 <outputs> | |
33 <data name="fel_log" format="txt" /> | |
34 <data name="fel_output" format="json" from_work_dir="fel_input.fa.FEL.json" /> | |
35 </outputs> | |
36 <tests> | |
37 <test> | |
38 <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> | |
39 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> | |
40 <output name="fel_output" file="fel-out1.json" compare="sim_size" /> | |
41 </test> | |
42 </tests> | |
43 <help> | |
44 <![CDATA[ | |
45 FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny. | |
46 ]]> | |
47 </help> | |
48 <expand macro="citations"> | |
49 <citation type="doi">10.1093/molbev/msi105</citation> | |
50 </expand> | |
51 </tool> |