annotate qiime2/qiime_fragment-insertion_sepp.xml @ 1:255f48db74f8 draft

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