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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_fastq-stats" name="qiime vsearch fastq-stats"
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3 version="2020.8">
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4 <description>Fastq stats with vsearch.</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 vsearch fastq-stats
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10
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11 --i-sequences=$isequences
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12
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13 #if str($pthreads) != 'None':
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14 --p-threads=$pthreads
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15 #end if
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16
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17 --o-visualization=ovisualization
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18
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19 #if str($examples) != 'None':
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20 --examples=$examples
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21 #end if
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22
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23 ;
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24 cp odereplicatedsequences.qza $odereplicatedsequences
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25
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26 ;
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27 qiime tools export ovisualization.qzv --output-path out
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28 && mkdir -p '$ovisualization.files_path'
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29 && cp -r out/* '$ovisualization.files_path'
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30 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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31
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32 ]]></command>
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33 <inputs>
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34 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] Fastq sequences [required]" name="isequences" optional="False" type="data" />
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35 <param label="--p-threads: " name="pthreads" optional="True" type="select">
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36 <option selected="True" value="None">Selection is Optional</option>
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37 <option value="Int % Range(1">Int % Range(1</option>
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38 <option value="None">None</option>
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39 </param>
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40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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46
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47 </outputs>
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48
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49 <help><![CDATA[
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50 Fastq stats with vsearch.
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51 ###############################################################
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52
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53 A fastq overview via vsearch's fastq_stats, fastq_eestats and
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54 fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch
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55 for detailed documentation of these tools.
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56
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57 Parameters
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58 ----------
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59 sequences : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
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60 Fastq sequences
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61 threads : Int % Range(1, None) | Str % Choices('auto'), optional
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62 The number of threads used for computation.
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63
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64 Returns
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65 -------
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66 visualization : Visualization
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67 ]]></help>
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68 <macros>
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69 <import>qiime_citation.xml</import>
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70 </macros>
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71 <expand macro="qiime_citation"/>
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72 </tool> |
