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comparison qiime2/qiime_phylogeny_fasttree.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_phylogeny_fasttree" name="qiime phylogeny fasttree" version="2019.4">
3 <description> - Construct a phylogenetic tree with FastTree.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime phylogeny fasttree
9
10 --i-alignment=$ialignment
11
12 #set $pnthreads = '${GALAXY_SLOTS:-4}'
13 #if str($pnthreads):
14 --p-n-threads="$pnthreads"
15 #end if
16
17 --o-tree=otree
18 ;
19 cp otree.qza $otree
20 ]]></command>
21 <inputs>
22 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data"/>
23 </inputs>
24 <outputs>
25 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
26 </outputs>
27 <help><![CDATA[
28 Construct a phylogenetic tree with FastTree.
29 ############################################
30
31 Construct a phylogenetic tree with FastTree.
32
33 Parameters
34 ----------
35 alignment : FeatureData[AlignedSequence]
36 Aligned sequences to be used for phylogenetic reconstruction.
37
38 Returns
39 -------
40 tree : Phylogeny[Unrooted]
41 The resulting phylogenetic tree.
42 ]]></help>
43 <macros>
44 <import>qiime_citation.xml</import>
45 </macros>
46 <expand macro="qiime_citation"/>
47 </tool>