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comparison qiime_phylogeny_fasttree.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree" version="2018.4">
3 <description> - Construct a phylogenetic tree with FastTree.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime phylogeny fasttree --i-alignment=$ialignment
10 #set $pnthreads = '${GALAXY_SLOTS:-4}'
11
12 #if str($pnthreads):
13 --p-n-threads="$pnthreads"
14 #end if
15
16 #if str($cmdconfig) != 'None':
17 --cmd-config=$cmdconfig
18 #end if
19 --o-tree=otree;
20 cp otree.qza $otree;
21 ]]>
22 </command>
23 <inputs>
24 <param format="qza,no_unzip.zip" label="--i-alignment: FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data"/>
25 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
26 </inputs>
27 <outputs>
28 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
29 </outputs>
30 <help>
31 <![CDATA[
32 Construct a phylogenetic tree with FastTree.
33 ---------------------------------------------
34
35 Construct a phylogenetic tree with FastTree.
36
37 Parameters
38 ----------
39 alignment : FeatureData[AlignedSequence]
40 Aligned sequences to be used for phylogenetic reconstruction.
41
42 Returns
43 -------
44 tree : Phylogeny[Unrooted]
45 The resulting phylogenetic tree.
46 ]]>
47 </help>
48 </tool>