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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2019.7">
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3 <description> - Compare query (observed) vs. reference (expected) sequences.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime quality-control evaluate-seqs
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9
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10 --i-query-sequences=$iquerysequences
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11 --i-reference-sequences=$ireferencesequences
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12
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13 --o-visualization=ovisualization
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14 ;
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15 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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16 && cp -r out/* '$ovisualization.files_path'
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17 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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18 ]]></command>
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19 <inputs>
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20 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data"/>
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21 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
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22 </inputs>
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23 <outputs>
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24 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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25 </outputs>
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26 <help><![CDATA[
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27 Compare query (observed) vs. reference (expected) sequences.
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28 ############################################################
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29
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30 This action aligns a set of query (e.g., observed) sequences against a set
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31 of reference (e.g., expected) sequences to evaluate the quality of
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32 alignment. The intended use is to align observed sequences against expected
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33 sequences (e.g., from a mock community) to determine the frequency of
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34 mismatches between observed sequences and the most similar expected
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35 sequences, e.g., as a measure of sequencing/method error. However, any
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36 sequences may be provided as input to generate a report on pairwise
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37 alignment quality against a set of reference sequences.
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38
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39 Parameters
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40 ----------
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41 query_sequences : FeatureData[Sequence]
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42 Sequences to test for exclusion
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43 reference_sequences : FeatureData[Sequence]
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44 Reference sequences to align against feature sequences
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45 show_alignments : Bool, optional
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46 Option to plot pairwise alignments of query sequences and their top
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47 hits.
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48
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49 Returns
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50 -------
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51 visualization : Visualization
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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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