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