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

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mafft-add" name="qiime alignment mafft-add"
3 version="2020.8">
4 <description>Add sequences to 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-add
10
11 --i-alignment=$ialignment
12
13 --i-sequences=$isequences
14
15 #if str($pnthreads) != 'None':
16 --p-n-threads=$pnthreads
17 #end if
18
19 #if $pparttree:
20 --p-parttree
21 #end if
22
23 --o-expanded-alignment=oexpandedalignment
24
25 #if str($examples) != 'None':
26 --examples=$examples
27 #end if
28
29 ;
30 cp oexpandedalignment.qza $oexpandedalignment
31
32 ]]></command>
33 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to which sequences should be added. [required]" name="ialignment" optional="False" type="data" />
35 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be added. [required]" name="isequences" optional="False" type="data" />
36 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
37 <option selected="True" value="None">Selection is Optional</option>
38 <option value="Int % Range(1">Int % Range(1</option>
39 <option value="None">None</option>
40 </param>
41 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean" />
42 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
43
44 </inputs>
45
46 <outputs>
47 <data format="qza" label="${tool.name} on ${on_string}: expandedalignment.qza" name="oexpandedalignment" />
48
49 </outputs>
50
51 <help><![CDATA[
52 Add sequences to multiple sequence alignment with MAFFT.
53 ###############################################################
54
55 Add new sequences to an existing alignment with MAFFT.
56
57 Parameters
58 ----------
59 alignment : FeatureData[AlignedSequence]
60 The alignment to which sequences should be added.
61 sequences : FeatureData[Sequence]
62 The sequences to be added.
63 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
64 The number of threads. (Use `auto` to automatically use all available
65 cores)
66 parttree : Bool, optional
67 This flag is required if the number of sequences being aligned are
68 larger than 1000000. Disabled by default
69
70 Returns
71 -------
72 expanded_alignment : FeatureData[AlignedSequence]
73 Alignment containing the provided aligned and unaligned sequences.
74 ]]></help>
75 <macros>
76 <import>qiime_citation.xml</import>
77 </macros>
78 <expand macro="qiime_citation"/>
79 </tool>