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1 <?xml version="1.0" ?>
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2 <tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp"
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3 version="2020.8">
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4 <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime fragment-insertion sepp
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10
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11 --i-representative-sequences=$irepresentativesequences
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12
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13 --i-reference-database=$ireferencedatabase
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15 --p-alignment-subset-size=$palignmentsubsetsize
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16
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17 --p-placement-subset-size=$pplacementsubsetsize
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18
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19 --p-threads=$pthreads
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20
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21 #if $pdebug:
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22 --p-debug
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23 #end if
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24
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25 --o-tree=otree
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26
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27 --o-placements=oplacements
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28
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29 #if str($examples) != 'None':
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30 --examples=$examples
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31 #end if
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32
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33 ;
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34 cp oplacements.qza $oplacements
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35
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36 ]]></command>
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37 <inputs>
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38 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert into the reference tree. [required]" name="irepresentativesequences" optional="False" type="data" />
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39 <param format="qza,no_unzip.zip" label="--i-reference-database: ARTIFACT SeppReferenceDatabase The reference database to insert the representative sequences into. [required]" name="ireferencedatabase" optional="False" type="data" />
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40 <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000" />
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41 <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/s epp-tutorial.md#sample-datasets-default-parameters. [default: 5000]" name="pplacementsubsetsize" optional="True" type="integer" value="5000" />
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42 <param label="--p-debug: --p-debug: / --p-no-debug Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]" name="pdebug" selected="False" type="boolean" />
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43 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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44
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45 </inputs>
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46
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47 <outputs>
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48 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
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49 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements" />
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50
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51 </outputs>
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52
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53 <help><![CDATA[
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54 Insert fragment sequences using SEPP into reference phylogenies.
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55 ###############################################################
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56
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57 Perform fragment insertion of sequences using the SEPP algorithm.
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58
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59 Parameters
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60 ----------
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61 representative_sequences : FeatureData[Sequence]
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62 The sequences to insert into the reference tree.
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63 reference_database : SeppReferenceDatabase
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64 The reference database to insert the representative sequences into.
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65 alignment_subset_size : Int, optional
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66 Each placement subset is further broken into subsets of at most these
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67 many sequences and a separate HMM is trained on each subset.
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68 placement_subset_size : Int, optional
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69 The tree is divided into subsets such that each subset includes at most
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70 these many subsets. The placement step places the fragment on only one
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71 subset, determined based on alignment scores. Further reading:
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72 https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
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73 tutorial.md#sample-datasets-default-parameters.
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74 threads : Int, optional
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75 The number of threads to use.
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76 debug : Bool, optional
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77 Collect additional run information to STDOUT for debugging. Temporary
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78 directories will not be removed if run fails.
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79
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80 Returns
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81 -------
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82 tree : Phylogeny[Rooted]
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83 The tree with inserted feature data.
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84 placements : Placements
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85 Information about the feature placements within the reference tree.
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86 ]]></help>
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87 <macros>
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88 <import>qiime_citation.xml</import>
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89 </macros>
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90 <expand macro="qiime_citation"/>
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91 </tool> |
