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comparison qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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" version="2019.4">
3 <description> - Build a phylogenetic tree using fasttree and mafft alignment</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime phylogeny align-to-tree-mafft-fasttree
9
10 --i-sequences=$isequences
11
12 #set $pnthreads = '${GALAXY_SLOTS:-4}'
13
14 #if str($pnthreads):
15 --p-n-threads="$pnthreads"
16 #end if
17
18
19 #if $pmaskmaxgapfrequency:
20 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
21 #end if
22
23 #if $pmaskminconservation:
24 --p-mask-min-conservation=$pmaskminconservation
25 #end if
26
27 --o-alignment=oalignment
28 --o-masked-alignment=omaskedalignment
29 --o-tree=otree
30 --o-rooted-tree=orootedtree
31 ;
32 cp oalignment.qza $oalignment;
33 cp omaskedalignment.qza $omaskedalignment;
34 cp otree.qza $otree;
35 cp orootedtree.qza $orootedtree
36 ]]></command>
37 <inputs>
38 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data"/>
39 <param label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" name="pmaskmaxgapfrequency" optional="True" type="float" min="0" max="1" exclusive_end="False" value="1.0"/>
40 <param label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" name="pmaskminconservation" optional="True" type="float" min="0" max="1" exclusive_end="False" value="0.4"/>
41 </inputs>
42 <outputs>
43 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/>
44 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/>
45 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
46 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree"/>
47 </outputs>
48 <help><![CDATA[
49 Build a phylogenetic tree using fasttree and mafft alignment
50 ############################################################
51
52 This pipeline will start by creating a sequence alignment using MAFFT,
53 after which any alignment columns that are phylogenetically uninformative
54 or ambiguously aligned will be removed (masked). The resulting masked
55 alignment will be used to infer a phylogenetic tree and then subsequently
56 rooted at its midpoint. Output files from each step of the pipeline will be
57 saved. This includes both the unmasked and masked MAFFT alignment from
58 q2-alignment methods, and both the rooted and unrooted phylogenies from
59 q2-phylogeny methods.
60
61 Parameters
62 ----------
63 sequences : FeatureData[Sequence]
64 The sequences to be used for creating a fasttree based rooted
65 phylogenetic tree.
66 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
67 The maximum relative frequency of gap characters in a column for the
68 column to be retained. This relative frequency must be a number between
69 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
70 gap characters, and 1.0 retains all columns regardless of gap
71 character frequency. This value is used when masking the aligned
72 sequences.
73 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
74 The minimum relative frequency of at least one non-gap character in a
75 column for that column to be retained. This relative frequency must be
76 a number between 0.0 and 1.0 (inclusive). For example, if a value of
77 0.4 is provided, a column will only be retained if it contains at
78 least one character that is present in at least 40% of the sequences.
79 This value is used when masking the aligned sequences.
80
81 Returns
82 -------
83 alignment : FeatureData[AlignedSequence]
84 The aligned sequences.
85 masked_alignment : FeatureData[AlignedSequence]
86 The masked alignment.
87 tree : Phylogeny[Unrooted]
88 The unrooted phylogenetic tree.
89 rooted_tree : Phylogeny[Rooted]
90 The rooted phylogenetic tree.
91 ]]></help>
92 <macros>
93 <import>qiime_citation.xml</import>
94 </macros>
95 <expand macro="qiime_citation"/>
96 </tool>