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comparison qiime2/qiime_alignment_mafft.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.4">
3 <description> - De novo multiple sequence alignment with MAFFT</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime alignment mafft
9
10 --i-sequences=$isequences
11 --o-alignment=oalignment
12
13 #set $pnthreads = '${GALAXY_SLOTS:-4}'
14
15 #if str($pnthreads):
16 --p-n-threads="$pnthreads"
17 #end if
18
19
20 #if $pparttree:
21 --p-parttree
22 #end if
23 ;
24 cp oalignment.qza $oalignment
25 ]]></command>
26 <inputs>
27 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data"/>
28 <param label="--p-parttree: --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean"/>
29 </inputs>
30 <outputs>
31 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/>
32 </outputs>
33 <help><![CDATA[
34 De novo multiple sequence alignment with MAFFT
35 ##############################################
36
37 Perform de novo multiple sequence alignment using MAFFT.
38
39 Parameters
40 ----------
41 sequences : FeatureData[Sequence]
42 The sequences to be aligned.
43 parttree : Bool, optional
44 This flag is required if the number of sequences being aligned are
45 larger than 1000000. Disabled by default
46
47 Returns
48 -------
49 alignment : FeatureData[AlignedSequence]
50 The aligned sequences.
51 ]]></help>
52 <macros>
53 <import>qiime_citation.xml</import>
54 </macros>
55 <expand macro="qiime_citation"/>
56 </tool>