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1 <?xml version="1.0" ?>
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2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2018.4">
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3 <description> - De novo multiple sequence alignment with MAFFT</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><![CDATA[
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8
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9 qiime alignment mafft --i-sequences=$isequences
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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
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20 --o-alignment=oalignment;
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21
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22 cp oalignment.qza $oalignment
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23
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24 ]]></command>
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25 <inputs>
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26 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] - The sequences to be aligned. [required]" name="isequences" optional="False" type="data"/>
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27 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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28 </inputs>
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29 <outputs>
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30 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/>
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31 </outputs>
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32 <help><![CDATA[
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33 De novo multiple sequence alignment with MAFFT
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34 ----------------------------------------------
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35
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36 Perform de novo multiple sequence alignment using MAFFT.
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37
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38 Parameters
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39 ----------
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40 sequences : FeatureData[Sequence]
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41 The sequences to be aligned.
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42
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43 Returns
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44 -------
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45 alignment : FeatureData[AlignedSequence]
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46 The aligned sequences.
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47 ]]>
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48 </help>
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49 </tool>
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