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comparison qiime2/qiime_phylogeny_align-to-tree-mafft-raxml.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_align-to-tree-mafft-raxml" name="qiime phylogeny align-to-tree-mafft-raxml"
3 version="2020.8">
4 <description>Build a phylogenetic tree using raxml 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-raxml
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 $pparttree:
22 --p-parttree
23 #end if
24
25 #if str($psubstitutionmodel) != 'None':
26 --p-substitution-model=$psubstitutionmodel
27 #end if
28
29 #if str($pseed):
30 --p-seed=$pseed
31 #end if
32 #if str($praxmlversion) != 'None':
33 --p-raxml-version=$praxmlversion
34 #end if
35
36 --o-alignment=oalignment
37
38 --o-masked-alignment=omaskedalignment
39
40 --o-tree=otree
41
42 --o-rooted-tree=orootedtree
43
44 #if str($examples) != 'None':
45 --examples=$examples
46 #end if
47
48 ;
49 cp orootedtree.qza $orootedtree
50
51 ]]></command>
52 <inputs>
53 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" />
54 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
55 <option selected="True" value="None">Selection is Optional</option>
56 <option value="Int % Range(1">Int % Range(1</option>
57 <option value="None">None</option>
58 </param>
59 <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" />
60 <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" />
61 <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. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline. [default: False]" name="pparttree" selected="False" type="boolean" />
62 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
63 <option selected="True" value="None">Selection is Optional</option>
64 <option value="GTRGAMMA">GTRGAMMA</option>
65 <option value="GTRGAMMAI">GTRGAMMAI</option>
66 <option value="GTRCAT">GTRCAT</option>
67 <option value="GTRCATI">GTRCATI</option>
68 </param>
69 <param label="--p-seed: INTEGER Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
70 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
71 <option selected="True" value="None">Selection is Optional</option>
72 <option value="Standard">Standard</option>
73 <option value="SSE3">SSE3</option>
74 <option value="AVX2">AVX2</option>
75 </param>
76 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
77
78 </inputs>
79
80 <outputs>
81 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
82 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
83 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
84 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
85
86 </outputs>
87
88 <help><![CDATA[
89 Build a phylogenetic tree using raxml and mafft alignment.
90 ###############################################################
91
92 This pipeline will start by creating a sequence alignment using MAFFT,
93 after which any alignment columns that are phylogenetically uninformative
94 or ambiguously aligned will be removed (masked). The resulting masked
95 alignment will be used to infer a phylogenetic tree using RAxML, under the
96 specified substitution model, and then subsequently rooted at its midpoint.
97 Output files from each step of the pipeline will be saved. This includes
98 both the unmasked and masked MAFFT alignment from q2-alignment methods, and
99 both the rooted and unrooted phylogenies from q2-phylogeny methods.
100
101 Parameters
102 ----------
103 sequences : FeatureData[Sequence]
104 The sequences to be used for creating a iqtree based rooted
105 phylogenetic tree.
106 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
107 The number of threads. (Use `all` to automatically use all available
108 cores. This value is used when aligning the sequences and creating the
109 tree with iqtree.
110 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
111 The maximum relative frequency of gap characters in a column for the
112 column to be retained. This relative frequency must be a number between
113 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
114 gap characters, and 1.0 retains all columns regardless of gap
115 character frequency. This value is used when masking the aligned
116 sequences.
117 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
118 The minimum relative frequency of at least one non-gap character in a
119 column for that column to be retained. This relative frequency must be
120 a number between 0.0 and 1.0 (inclusive). For example, if a value of
121 0.4 is provided, a column will only be retained if it contains at
122 least one character that is present in at least 40% of the sequences.
123 This value is used when masking the aligned sequences.
124 parttree : Bool, optional
125 This flag is required if the number of sequences being aligned are
126 larger than 1000000. Disabled by default. NOTE: if using this option,
127 it is recomended that only the CAT-based substitution models of RAxML
128 be considered for this pipeline.
129 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
130 Model of Nucleotide Substitution.
131 seed : Int, optional
132 Random number seed for the parsimony starting tree. This allows you to
133 reproduce tree results. If not supplied then one will be randomly
134 chosen.
135 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
136 Select a specific CPU optimization of RAxML to use. The SSE3 versions
137 will run approximately 40% faster than the standard version. The AVX2
138 version will run 10-30% faster than the SSE3 version.
139
140 Returns
141 -------
142 alignment : FeatureData[AlignedSequence]
143 The aligned sequences.
144 masked_alignment : FeatureData[AlignedSequence]
145 The masked alignment.
146 tree : Phylogeny[Unrooted]
147 The unrooted phylogenetic tree.
148 rooted_tree : Phylogeny[Rooted]
149 The rooted phylogenetic tree.
150 ]]></help>
151 <macros>
152 <import>qiime_citation.xml</import>
153 </macros>
154 <expand macro="qiime_citation"/>
155 </tool>