Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_alignment_mafft.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
parents | 276ec629f09a |
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28:c28331a63dfd | 29:3ba9833030c1 |
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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> |