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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="2018.4">
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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="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 quality-control evaluate-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences
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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
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14 #if $pshowalignments:
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15 --p-show-alignments
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16 #else
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17 --p-no-show-alignments
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18 #end if
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19
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20 #end if
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21 --o-visualization=ovisualization;
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22
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23 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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24 && cp -r out/* '$ovisualization.files_path'
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25 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param format="qza,no_unzip.zip" label="--i-query-sequences: FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data"/>
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30 <param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
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31
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32 <param label=" --p-show-alignments / --p-no-show-alignments
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33 Option to plot pairwise alignments of query
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34 sequences and their top hits. [default:
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35 False]" name="pshowalignments" checked="False" type="boolean"/>
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36
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37 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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38 </inputs>
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39 <outputs>
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40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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41 </outputs>
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42 <help>
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43 <![CDATA[
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44 Compare query (observed) vs. reference (expected) sequences.
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45 -------------------------------------------------------------
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46
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47 This action aligns a set of query (e.g., observed) sequences against a set
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48 of reference (e.g., expected) sequences to evaluate the quality of
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49 alignment. The intended use is to align observed sequences against expected
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50 sequences (e.g., from a mock community) to determine the frequency of
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51 mismatches between observed sequences and the most similar expected
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52 sequences, e.g., as a measure of sequencing/method error. However, any
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53 sequences may be provided as input to generate a report on pairwise
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54 alignment quality against a set of reference sequences.
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55
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56 Parameters
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57 ----------
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58 query_sequences : FeatureData[Sequence]
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59 Sequences to test for exclusion
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60 reference_sequences : FeatureData[Sequence]
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61 Reference sequences to align against feature sequences
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62 show_alignments : Bool, optional
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63 Option to plot pairwise alignments of query sequences and their top
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64 hits.
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65
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66 Returns
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67 -------
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68 visualization : Visualization
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69 \
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70 ]]>
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71 </help>
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72 <macros>
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73 <import>qiime_citation.xml</import>
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74 </macros>
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75 <expand macro="qiime_citation" />
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76 </tool>
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