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comparison qiime2/qiime_alignment_mafft.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
parents 276ec629f09a
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28:c28331a63dfd 29:3ba9833030c1
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>