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