Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_fragment-insertion_sepp.xml @ 0:370e0b6e9826 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children 914fa4daf16a
comparison
equal deleted inserted replaced
-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp" version="2019.4">
3 <description> - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime fragment-insertion sepp
9
10 --i-representative-sequences=$irepresentativesequences
11
12 #if str($ireferencealignment) != 'None':
13 --i-reference-alignment=$ireferencealignment
14 #end if
15
16 #if str($ireferencephylogeny) != 'None':
17 --i-reference-phylogeny=$ireferencephylogeny
18 #end if
19
20 #set $pthreads = '${GALAXY_SLOTS:-4}'
21 #if str($pthreads):
22 --p-threads="$pthreads"
23 #end if
24
25
26 #if $palignmentsubsetsize:
27 --p-alignment-subset-size=$palignmentsubsetsize
28 #end if
29
30 #if str($pplacementsubsetsize):
31 --p-placement-subset-size="$pplacementsubsetsize"
32 #end if
33
34 #if $pdebug:
35 --p-debug
36 #end if
37
38 --o-tree=otree
39 --o-placements=oplacements
40 ;
41 cp otree.qza $otree;
42 cp oplacements.qza $oplacements
43 ]]></command>
44 <inputs>
45 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert [required]" name="irepresentativesequences" optional="False" type="data"/>
46 <param format="qza,no_unzip.zip" label="--i-reference-alignment: ARTIFACT FeatureData[AlignedSequence] The reference multiple nucleotide alignment used to construct the reference phylogeny. [optional]" name="ireferencealignment" optional="True" type="data"/>
47 <param format="qza,no_unzip.zip" label="--i-reference-phylogeny: ARTIFACT Phylogeny[Rooted] The rooted reference phylogeny. Must be in sync with reference-alignment, i.e. each tip name must have exactly one corresponding record. [optional]" name="ireferencephylogeny" optional="True" type="data"/>
48 <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time. [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000"/>
49 <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large." name="pplacementsubsetsize" optional="True" type="integer"/>
50 <param label="--p-debug: --p-no-debug Print additional run information to STDOUT for debugging. Run together with --verbose to actually see the information on STDOUT. Temporary directories will not be removed if run fails. [default: False]" name="pdebug" selected="False" type="boolean"/>
51 </inputs>
52 <outputs>
53 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
54 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements"/>
55 </outputs>
56 <help><![CDATA[
57 Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8
58 ####################################################################################
59
60 Perform fragment insertion of 16S sequences using the SEPP algorithm
61 against the Greengenes 13_8 99% tree.
62
63 Parameters
64 ----------
65 representative_sequences : FeatureData[Sequence]
66 The sequences to insert
67 alignment_subset_size : Int, optional
68 Each placement subset is further broken into subsets of at most these
69 many sequences and a separate HMM is trained on each subset. The
70 default alignment subset size is set to balance the exhaustiveness of
71 the alignment step with the running time.
72 placement_subset_size : Int, optional
73 The tree is divided into subsets such that each subset includes at most
74 these many subsets. The placement step places the fragment on only one
75 subset, determined based on alignment scores. The default placement
76 subset is set to make sure the memory requirement of the pplacer step
77 does not become prohibitively large. Further reading:
78 https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
79 tutorial.md#sample-datasets-default-parameters
80 reference_alignment : FeatureData[AlignedSequence], optional
81 The reference multiple nucleotide alignment used to construct the
82 reference phylogeny.
83 reference_phylogeny : Phylogeny[Rooted], optional
84 The rooted reference phylogeny. Must be in sync with reference-
85 alignment, i.e. each tip name must have exactly one corresponding
86 record.
87 debug : Bool, optional
88 Print additional run information to STDOUT for debugging. Run together
89 with --verbose to actually see the information on STDOUT. Temporary
90 directories will not be removed if run fails.
91
92 Returns
93 -------
94 tree : Phylogeny[Rooted]
95 The tree with inserted feature data
96 placements : Placements
97 \
98 ]]></help>
99 <macros>
100 <import>qiime_citation.xml</import>
101 </macros>
102 <expand macro="qiime_citation"/>
103 </tool>