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comparison qiime2-2020.8/qiime_fragment-insertion_sepp.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp"
3 version="2020.8">
4 <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime fragment-insertion sepp
10
11 --i-representative-sequences=$irepresentativesequences
12
13 --i-reference-database=$ireferencedatabase
14
15 --p-alignment-subset-size=$palignmentsubsetsize
16
17 --p-placement-subset-size=$pplacementsubsetsize
18
19 --p-threads=$pthreads
20
21 #if $pdebug:
22 --p-debug
23 #end if
24
25 --o-tree=otree
26
27 --o-placements=oplacements
28
29 #if str($examples) != 'None':
30 --examples=$examples
31 #end if
32
33 ;
34 cp oplacements.qza $oplacements
35
36 ]]></command>
37 <inputs>
38 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert into the reference tree. [required]" name="irepresentativesequences" optional="False" type="data" />
39 <param format="qza,no_unzip.zip" label="--i-reference-database: ARTIFACT SeppReferenceDatabase The reference database to insert the representative sequences into. [required]" name="ireferencedatabase" optional="False" type="data" />
40 <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000" />
41 <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/s epp-tutorial.md#sample-datasets-default-parameters. [default: 5000]" name="pplacementsubsetsize" optional="True" type="integer" value="5000" />
42 <param label="--p-debug: --p-debug: / --p-no-debug Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]" name="pdebug" selected="False" type="boolean" />
43 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
44
45 </inputs>
46
47 <outputs>
48 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
49 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements" />
50
51 </outputs>
52
53 <help><![CDATA[
54 Insert fragment sequences using SEPP into reference phylogenies.
55 ###############################################################
56
57 Perform fragment insertion of sequences using the SEPP algorithm.
58
59 Parameters
60 ----------
61 representative_sequences : FeatureData[Sequence]
62 The sequences to insert into the reference tree.
63 reference_database : SeppReferenceDatabase
64 The reference database to insert the representative sequences into.
65 alignment_subset_size : Int, optional
66 Each placement subset is further broken into subsets of at most these
67 many sequences and a separate HMM is trained on each subset.
68 placement_subset_size : Int, optional
69 The tree is divided into subsets such that each subset includes at most
70 these many subsets. The placement step places the fragment on only one
71 subset, determined based on alignment scores. Further reading:
72 https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
73 tutorial.md#sample-datasets-default-parameters.
74 threads : Int, optional
75 The number of threads to use.
76 debug : Bool, optional
77 Collect additional run information to STDOUT for debugging. Temporary
78 directories will not be removed if run fails.
79
80 Returns
81 -------
82 tree : Phylogeny[Rooted]
83 The tree with inserted feature data.
84 placements : Placements
85 Information about the feature placements within the reference tree.
86 ]]></help>
87 <macros>
88 <import>qiime_citation.xml</import>
89 </macros>
90 <expand macro="qiime_citation"/>
91 </tool>