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comparison qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree"
3 version="2020.8">
4 <description>Build a phylogenetic tree using fasttree and mafft alignment</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny align-to-tree-mafft-fasttree
10
11 --i-sequences=$isequences
12
13 #if str($pnthreads) != 'None':
14 --p-n-threads=$pnthreads
15 #end if
16
17 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
18
19 --p-mask-min-conservation=$pmaskminconservation
20
21 #if $pparttree:
22 --p-parttree
23 #end if
24
25 --o-alignment=oalignment
26
27 --o-masked-alignment=omaskedalignment
28
29 --o-tree=otree
30
31 --o-rooted-tree=orootedtree
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
37 ;
38 cp orootedtree.qza $orootedtree
39
40 ]]></command>
41 <inputs>
42 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" />
43 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
44 <option selected="True" value="None">Selection is Optional</option>
45 <option value="Int % Range(1">Int % Range(1</option>
46 <option value="None">None</option>
47 </param>
48 <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
49 <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
50 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]" name="pparttree" selected="False" type="boolean" />
51 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
52
53 </inputs>
54
55 <outputs>
56 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
57 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
58 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
59 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
60
61 </outputs>
62
63 <help><![CDATA[
64 Build a phylogenetic tree using fasttree and mafft alignment
65 ###############################################################
66
67 This pipeline will start by creating a sequence alignment using MAFFT,
68 after which any alignment columns that are phylogenetically uninformative
69 or ambiguously aligned will be removed (masked). The resulting masked
70 alignment will be used to infer a phylogenetic tree and then subsequently
71 rooted at its midpoint. Output files from each step of the pipeline will be
72 saved. This includes both the unmasked and masked MAFFT alignment from
73 q2-alignment methods, and both the rooted and unrooted phylogenies from
74 q2-phylogeny methods.
75
76 Parameters
77 ----------
78 sequences : FeatureData[Sequence]
79 The sequences to be used for creating a fasttree based rooted
80 phylogenetic tree.
81 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
82 The number of threads. (Use `auto` to automatically use all available
83 cores) This value is used when aligning the sequences and creating the
84 tree with fasttree.
85 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
86 The maximum relative frequency of gap characters in a column for the
87 column to be retained. This relative frequency must be a number between
88 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
89 gap characters, and 1.0 retains all columns regardless of gap
90 character frequency. This value is used when masking the aligned
91 sequences.
92 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
93 The minimum relative frequency of at least one non-gap character in a
94 column for that column to be retained. This relative frequency must be
95 a number between 0.0 and 1.0 (inclusive). For example, if a value of
96 0.4 is provided, a column will only be retained if it contains at
97 least one character that is present in at least 40% of the sequences.
98 This value is used when masking the aligned sequences.
99 parttree : Bool, optional
100 This flag is required if the number of sequences being aligned are
101 larger than 1000000. Disabled by default.
102
103 Returns
104 -------
105 alignment : FeatureData[AlignedSequence]
106 The aligned sequences.
107 masked_alignment : FeatureData[AlignedSequence]
108 The masked alignment.
109 tree : Phylogeny[Unrooted]
110 The unrooted phylogenetic tree.
111 rooted_tree : Phylogeny[Rooted]
112 The rooted phylogenetic tree.
113 ]]></help>
114 <macros>
115 <import>qiime_citation.xml</import>
116 </macros>
117 <expand macro="qiime_citation"/>
118 </tool>