Mercurial > repos > iuc > hyphy_gard

comparison hyphy_gard.xml @ 1:a03d87763f51 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author iuc
date Thu, 13 Feb 2020 15:00:59 -0500
parents 1942d02039c2
children 728d5b0af60f
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0:1942d02039c2 1:a03d87763f51
17 #end if 17 #end if
18 --rv '$rate_cond.rate' 18 --rv '$rate_cond.rate'
19 #if str($rate_cond.rate) != 'None': 19 #if str($rate_cond.rate) != 'None':
20 --rate-classes '$rate_classes' 20 --rate-classes '$rate_classes'
21 #end if 21 #end if
22 --output '$translated'
23 --output-lf '$gard_output'
22 > '$gard_log' 24 > '$gard_log'
23 ]]></command> 25 ]]></command>
24 <inputs> 26 <inputs>
25 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 27 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
26 <conditional name="datatype"> 28 <conditional name="datatype">
27 <param name="value" type="select" label="Type of data"> 29 <param name="value" type="select" label="Type of data">
28 <option value="Nucleotide">Nucleotide</option> 30 <option value="nucleotide">Nucleotide</option>
29 <option value="Protein">Amino acid</option> 31 <option value="protein">Amino acid</option>
30 <option value="Codon">Codon</option> 32 <option value="codon">Codon</option>
31 </param> 33 </param>
32 <when value="Nucleotide"/> 34 <when value="Nucleotide"/>
33 <when value="Protein"> 35 <when value="Protein">
34 <expand macro="substitution" /> 36 <expand macro="substitution" />
35 </when> 37 </when>
52 </when> 54 </when>
53 </conditional> 55 </conditional>
54 </inputs> 56 </inputs>
55 <outputs> 57 <outputs>
56 <data name="gard_log" format="txt"/> 58 <data name="gard_log" format="txt"/>
57 <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/> 59 <data name="gard_output" format="nex" />
58 <data name="translated" format="hyphy_results.json" from_work_dir="gard_input.fa.json"/> 60 <data name="translated" format="hyphy_results.json" />
59 </outputs> 61 </outputs>
60 <tests> 62 <tests>
61 <test> 63 <test>
62 <param name="input_file" ftype="fasta" value="gard-in1.fa"/> 64 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
63 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/> 65 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
64 </test> 66 </test>
65 </tests> 67 </tests>
66 <help><![CDATA[ 68 <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. 69 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.
70
71 See the online documentation_ for more information.
72
73 .. _documentation: http://hyphy.org/methods/selection-methods/#gard
68 ]]></help> 74 ]]></help>
69 <expand macro="citations"> 75 <expand macro="citations">
70 <citation type="doi">10.1093/molbev/msl051</citation> 76 <citation type="doi">10.1093/molbev/msl051</citation>
71 </expand> 77 </expand>
72 </tool> 78 </tool>