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1 <?xml version="1.0" ?>
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2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft"
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3 version="2020.8">
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4 <description>De novo multiple sequence alignment with MAFFT</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime alignment mafft
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10
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11 --i-sequences=$isequences
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12
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13 #if str($pnthreads) != 'None':
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14 --p-n-threads=$pnthreads
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15 #end if
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16
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17 #if $pparttree:
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18 --p-parttree
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19 #end if
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20
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21 --o-alignment=oalignment
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22
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23 #if str($examples) != 'None':
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24 --examples=$examples
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25 #end if
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26
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27 ;
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28 cp oalignment.qza $oalignment
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29
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30 ]]></command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data" />
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33 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
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34 <option selected="True" value="None">Selection is Optional</option>
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35 <option value="Int % Range(1">Int % Range(1</option>
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36 <option value="None">None</option>
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37 </param>
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38 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean" />
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39 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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40
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41 </inputs>
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42
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43 <outputs>
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44 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
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45
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46 </outputs>
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47
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48 <help><![CDATA[
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49 De novo multiple sequence alignment with MAFFT
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50 ###############################################################
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51
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52 Perform de novo multiple sequence alignment using MAFFT.
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53
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54 Parameters
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55 ----------
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56 sequences : FeatureData[Sequence]
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57 The sequences to be aligned.
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58 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
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59 The number of threads. (Use `auto` to automatically use all available
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60 cores)
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61 parttree : Bool, optional
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62 This flag is required if the number of sequences being aligned are
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63 larger than 1000000. Disabled by default
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64
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65 Returns
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66 -------
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67 alignment : FeatureData[AlignedSequence]
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68 The aligned sequences.
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69 ]]></help>
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70 <macros>
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71 <import>qiime_citation.xml</import>
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72 </macros>
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73 <expand macro="qiime_citation"/>
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74 </tool> |
