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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2018.4">
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3 <description> - Dereplicate sequences.</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 vsearch dereplicate-sequences --i-sequences=$isequences --o-dereplicated-sequences=odereplicatedsequences
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10
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11 #if str($cmdconfig) != 'None':
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12 --cmd-config=$cmdconfig
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13 #end if
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14 --o-dereplicated-table=odereplicatedtable;
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15
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16 cp odereplicatedsequences.qza $odereplicatedsequences;
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17 cp odereplicatedtable.qza $odereplicatedtable;
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="qza,no_unzip.zip" label="--i-sequences: SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data"/>
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22
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23 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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24 </inputs>
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25 <outputs>
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26 <data format="qza" label="${tool.name} on ${on_string}: dereplicated-sequences.qza" name="odereplicatedsequences"/>
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27 <data format="qza" label="${tool.name} on ${on_string}: dereplicated-table.qza" name="odereplicatedtable"/>
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28 </outputs>
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29 <help>
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30 <![CDATA[
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31 Dereplicate sequences.
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32 -----------------------
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33
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34 Dereplicate sequence data and create a feature table and feature
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35 representative sequences. Feature identfiers in the resulting artifacts
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36 will be the sha1 hash of the sequence defining each feature. If clustering
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37 of features into OTUs is desired, the resulting artifacts can be passed to
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38 the cluster_features_* methods in this plugin.
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39
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40 Parameters
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41 ----------
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42 sequences : SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences]
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43 The sequences to be dereplicated.
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44
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45 Returns
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46 -------
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47 dereplicated_table : FeatureTable[Frequency]
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48 The table of dereplicated sequences.
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49 dereplicated_sequences : FeatureData[Sequence]
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50 The dereplicated sequences.
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51 ]]>
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52 </help>
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53 <macros>
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54 <import>qiime_citation.xml</import>
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55 </macros>
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56 <expand macro="qiime_citation" />
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57 </tool>
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