Mercurial > repos > iuc > hyphy_gard
comparison hyphy_gard.xml @ 0:1942d02039c2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
| author | iuc |
|---|---|
| date | Wed, 21 Aug 2019 12:23:44 -0400 |
| parents | |
| children | a03d87763f51 |
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| -1:000000000000 | 0:1942d02039c2 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0"> | |
| 3 <description>Genetic Algorithm for Recombination Detection</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '$input_file' gard_input.fa && | |
| 10 @HYPHY_INVOCATION@ gard | |
| 11 --alignment ./gard_input.fa | |
| 12 --type '$datatype.value' | |
| 13 #if str($datatype.value) == 'Codon': | |
| 14 --code '$datatype.gencodeid' | |
| 15 #elif str($datatype.value) == 'Protein': | |
| 16 --model '$datatype.model' | |
| 17 #end if | |
| 18 --rv '$rate_cond.rate' | |
| 19 #if str($rate_cond.rate) != 'None': | |
| 20 --rate-classes '$rate_classes' | |
| 21 #end if | |
| 22 > '$gard_log' | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> | |
| 26 <conditional name="datatype"> | |
| 27 <param name="value" type="select" label="Type of data"> | |
| 28 <option value="Nucleotide">Nucleotide</option> | |
| 29 <option value="Protein">Amino acid</option> | |
| 30 <option value="Codon">Codon</option> | |
| 31 </param> | |
| 32 <when value="Nucleotide"/> | |
| 33 <when value="Protein"> | |
| 34 <expand macro="substitution" /> | |
| 35 </when> | |
| 36 <when value="Codon"> | |
| 37 <expand macro="gencode" /> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 <conditional name="rate_cond"> | |
| 41 <param name="rate" type="select" label="Rate variation"> | |
| 42 <option value="None">None</option> | |
| 43 <option value="GDD">General Discrete</option> | |
| 44 <option value="Gamma">Beta-Gamma</option> | |
| 45 </param> | |
| 46 <when value="None"/> | |
| 47 <when value="GDD"> | |
| 48 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/> | |
| 49 </when> | |
| 50 <when value="Gamma"> | |
| 51 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 </inputs> | |
| 55 <outputs> | |
| 56 <data name="gard_log" format="txt"/> | |
| 57 <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/> | |
| 58 <data name="translated" format="hyphy_results.json" from_work_dir="gard_input.fa.json"/> | |
| 59 </outputs> | |
| 60 <tests> | |
| 61 <test> | |
| 62 <param name="input_file" ftype="fasta" value="gard-in1.fa"/> | |
| 63 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help><![CDATA[ | |
| 67 GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block. | |
| 68 ]]></help> | |
| 69 <expand macro="citations"> | |
| 70 <citation type="doi">10.1093/molbev/msl051</citation> | |
| 71 </expand> | |
| 72 </tool> |