Mercurial > repos > iuc > hyphy_fel
comparison hyphy_fel.xml @ 1:6c3ece5fb602 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author | iuc |
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date | Wed, 21 Aug 2019 12:27:42 -0400 |
parents | 24a2bf70dbdd |
children | a8b34daec0d9 |
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0:24a2bf70dbdd | 1:6c3ece5fb602 |
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2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> | 2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> |
3 <description>Fixed Effects Likelihood</description> | 3 <description>Fixed Effects Likelihood</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="requirements"/> |
8 <expand macro="version_command" /> | 8 <command detect_errors="exit_code"><![CDATA[ |
9 <command detect_errors="exit_code"> | 9 ln -s '$input_file' fel_input.fa && |
10 <![CDATA[ | 10 ln -s '$input_nhx' fel_input.nhx && |
11 ln -s '$input_file' fel_input.fa && | 11 @HYPHY_INVOCATION@ fel |
12 ln -s '$input_nhx' fel_input.nhx && | 12 --alignment ./fel_input.fa |
13 echo $gencodeid > tool_params && | 13 --tree ./fel_input.nhx |
14 echo `pwd`/fel_input.fa >> tool_params && | 14 --code '$gencodeid' |
15 echo `pwd`/fel_input.nhx >> tool_params && | 15 --branches '$branches' |
16 echo '$branches' >> tool_params && | 16 --srv '$include_srv' |
17 echo '$include_srv' >> tool_params && | 17 --pvalue '$p_value' |
18 echo '$p_value' >> tool_params && | 18 > '$fel_log' |
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$fel_log' | 19 ]]></command> |
20 ]]> | |
21 </command> | |
22 <inputs> | 20 <inputs> |
23 <expand macro="inputs" /> | 21 <expand macro="inputs"/> |
24 <expand macro="gencode" /> | 22 <expand macro="gencode"/> |
25 <expand macro="branches" /> | 23 <expand macro="branches"/> |
26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> | 24 <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"> | 25 <param name="include_srv" type="select" label="Include synonymous rate variation"> |
28 <option value="1">Yes (recommended)</option> | 26 <option value="Yes">Yes (recommended)</option> |
29 <option value="2">No</option> | 27 <option value="No">No</option> |
30 </param> | 28 </param> |
31 </inputs> | 29 </inputs> |
32 <outputs> | 30 <outputs> |
33 <data name="fel_log" format="txt" /> | 31 <data name="fel_log" format="txt"/> |
34 <data name="fel_output" format="json" from_work_dir="fel_input.fa.FEL.json" /> | 32 <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.json"/> |
35 </outputs> | 33 </outputs> |
36 <tests> | 34 <tests> |
37 <test> | 35 <test> |
38 <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> | 36 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
39 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> | 37 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
40 <output name="fel_output" file="fel-out1.json" compare="sim_size" /> | 38 <output name="fel_output" file="fel-out1.json" compare="sim_size"/> |
41 </test> | 39 </test> |
42 </tests> | 40 </tests> |
43 <help> | 41 <help><![CDATA[ |
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. | 42 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 ]]> | 43 ]]></help> |
47 </help> | |
48 <expand macro="citations"> | 44 <expand macro="citations"> |
49 <citation type="doi">10.1093/molbev/msi105</citation> | 45 <citation type="doi">10.1093/molbev/msi105</citation> |
50 </expand> | 46 </expand> |
51 </tool> | 47 </tool> |