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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"
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3 version="2020.8">
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4 <description>Compare query (observed) vs. reference (expected) sequences.</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 quality-control evaluate-seqs
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10
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11 --i-query-sequences=$iquerysequences
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12
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13 --i-reference-sequences=$ireferencesequences
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14
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15 --o-visualization=ovisualization
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16
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17 #if str($examples) != 'None':
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18 --examples=$examples
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19 #end if
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20
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21 ;
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22 cp odatabase.qza $odatabase
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23
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24 ;
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25 qiime tools export ovisualization.qzv --output-path out
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26 && mkdir -p '$ovisualization.files_path'
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27 && cp -r out/* '$ovisualization.files_path'
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28 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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29
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30 ;
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31 qiime tools export ovisualization.qzv --output-path out
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32 && mkdir -p '$ovisualization.files_path'
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33 && cp -r out/* '$ovisualization.files_path'
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34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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35
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36 ]]></command>
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37 <inputs>
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38 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data" />
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39 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" />
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40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data format="html" label="${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 Compare query (observed) vs. reference (expected) sequences.
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51 ###############################################################
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52
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53 This action aligns a set of query (e.g., observed) sequences against a set
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54 of reference (e.g., expected) sequences to evaluate the quality of
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55 alignment. The intended use is to align observed sequences against expected
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56 sequences (e.g., from a mock community) to determine the frequency of
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57 mismatches between observed sequences and the most similar expected
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58 sequences, e.g., as a measure of sequencing/method error. However, any
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59 sequences may be provided as input to generate a report on pairwise
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60 alignment quality against a set of reference sequences.
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61
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62 Parameters
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63 ----------
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64 query_sequences : FeatureData[Sequence]
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65 Sequences to test for exclusion
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66 reference_sequences : FeatureData[Sequence]
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67 Reference sequences to align against feature sequences
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68 show_alignments : Bool, optional
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69 Option to plot pairwise alignments of query sequences and their top
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70 hits.
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71
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72 Returns
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73 -------
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74 visualization : Visualization
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75 ]]></help>
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76 <macros>
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77 <import>qiime_citation.xml</import>
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78 </macros>
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79 <expand macro="qiime_citation"/>
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80 </tool> |
