annotate hyphy_gard.xml @ 3:bff9a82d630d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6b2cd926797bb94fba9d0e319a2dbcff6ee37735"
author iuc
date Sun, 16 Feb 2020 00:00:54 -0500
parents 728d5b0af60f
children 6283babe736e
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
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3 <description>Genetic Algorithm for Recombination Detection</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_file' gard_input.fa &&
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10 @HYPHYMPI@ gard
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11 --alignment ./gard_input.fa
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12 --type '$datatype.value'
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13 #if str($datatype.value) == 'Codon':
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14 --code '$datatype.gencodeid'
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15 #elif str($datatype.value) == 'Protein':
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16 --model '$datatype.model'
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17 #end if
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18 --rv '$rate_cond.rate'
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19 #if str($rate_cond.rate) != 'None':
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20 --rate-classes '$rate_classes'
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21 #end if
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22 --output '$translated'
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23 --output-lf '$gard_output'
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24 > '$gard_log'
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25 ]]></command>
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26 <inputs>
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27 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
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28 <conditional name="datatype">
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29 <param name="value" type="select" label="Type of data">
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30 <option value="nucleotide">Nucleotide</option>
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31 <option value="protein">Amino acid</option>
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32 <option value="codon">Codon</option>
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33 </param>
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34 <when value="Nucleotide"/>
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35 <when value="Protein">
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36 <expand macro="substitution" />
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37 </when>
1942d02039c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <when value="Codon">
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39 <expand macro="gencode" />
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40 </when>
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41 </conditional>
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42 <conditional name="rate_cond">
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43 <param name="rate" type="select" label="Rate variation">
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44 <option value="None">None</option>
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45 <option value="GDD">General Discrete</option>
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46 <option value="Gamma">Beta-Gamma</option>
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47 </param>
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48 <when value="None"/>
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49 <when value="GDD">
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50 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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51 </when>
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52 <when value="Gamma">
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53 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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54 </when>
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55 </conditional>
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56 </inputs>
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57 <outputs>
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58 <data name="gard_log" format="txt"/>
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59 <data name="gard_output" format="nex" />
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60 <data name="translated" format="hyphy_results.json" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
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65 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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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.
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70
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71 See the online documentation_ for more information.
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72
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73 .. _documentation: http://hyphy.org/methods/selection-methods/#gard
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74 ]]></help>
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75 <expand macro="citations">
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76 <citation type="doi">10.1093/molbev/msl051</citation>
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77 </expand>
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78 </tool>