|
15
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft"
|
|
|
3 version="2020.8">
|
|
|
4 <description>De novo multiple sequence alignment with MAFFT</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime alignment mafft
|
|
|
10
|
|
|
11 --i-sequences=$isequences
|
|
|
12
|
|
|
13 #if str($pnthreads) != 'None':
|
|
|
14 --p-n-threads=$pnthreads
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if $pparttree:
|
|
|
18 --p-parttree
|
|
|
19 #end if
|
|
|
20
|
|
|
21 --o-alignment=oalignment
|
|
|
22
|
|
|
23 #if str($examples) != 'None':
|
|
|
24 --examples=$examples
|
|
|
25 #end if
|
|
|
26
|
|
|
27 ;
|
|
|
28 cp oalignment.qza $oalignment
|
|
|
29
|
|
|
30 ]]></command>
|
|
|
31 <inputs>
|
|
|
32 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data" />
|
|
|
33 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
|
|
|
34 <option selected="True" value="None">Selection is Optional</option>
|
|
|
35 <option value="Int % Range(1">Int % Range(1</option>
|
|
|
36 <option value="None">None</option>
|
|
|
37 </param>
|
|
|
38 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean" />
|
|
|
39 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
40
|
|
|
41 </inputs>
|
|
|
42
|
|
|
43 <outputs>
|
|
|
44 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
|
|
|
45
|
|
|
46 </outputs>
|
|
|
47
|
|
|
48 <help><![CDATA[
|
|
|
49 De novo multiple sequence alignment with MAFFT
|
|
|
50 ###############################################################
|
|
|
51
|
|
|
52 Perform de novo multiple sequence alignment using MAFFT.
|
|
|
53
|
|
|
54 Parameters
|
|
|
55 ----------
|
|
|
56 sequences : FeatureData[Sequence]
|
|
|
57 The sequences to be aligned.
|
|
|
58 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
|
|
|
59 The number of threads. (Use `auto` to automatically use all available
|
|
|
60 cores)
|
|
|
61 parttree : Bool, optional
|
|
|
62 This flag is required if the number of sequences being aligned are
|
|
|
63 larger than 1000000. Disabled by default
|
|
|
64
|
|
|
65 Returns
|
|
|
66 -------
|
|
|
67 alignment : FeatureData[AlignedSequence]
|
|
|
68 The aligned sequences.
|
|
|
69 ]]></help>
|
|
|
70 <macros>
|
|
|
71 <import>qiime_citation.xml</import>
|
|
|
72 </macros>
|
|
|
73 <expand macro="qiime_citation"/>
|
|
|
74 </tool> |
