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comparison qiime2-2020.8/qiime_quality-control_evaluate-seqs.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs"
3 version="2020.8">
4 <description>Compare query (observed) vs. reference (expected) sequences.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime quality-control evaluate-seqs
10
11 --i-query-sequences=$iquerysequences
12
13 --i-reference-sequences=$ireferencesequences
14
15 --o-visualization=ovisualization
16
17 #if str($examples) != 'None':
18 --examples=$examples
19 #end if
20
21 ;
22 cp odatabase.qza $odatabase
23
24 ;
25 qiime tools export ovisualization.qzv --output-path out
26 && mkdir -p '$ovisualization.files_path'
27 && cp -r out/* '$ovisualization.files_path'
28 && mv '$ovisualization.files_path/index.html' '$ovisualization'
29
30 ;
31 qiime tools export ovisualization.qzv --output-path out
32 && mkdir -p '$ovisualization.files_path'
33 && cp -r out/* '$ovisualization.files_path'
34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
35
36 ]]></command>
37 <inputs>
38 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data" />
39 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" />
40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
41
42 </inputs>
43
44 <outputs>
45 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
46
47 </outputs>
48
49 <help><![CDATA[
50 Compare query (observed) vs. reference (expected) sequences.
51 ###############################################################
52
53 This action aligns a set of query (e.g., observed) sequences against a set
54 of reference (e.g., expected) sequences to evaluate the quality of
55 alignment. The intended use is to align observed sequences against expected
56 sequences (e.g., from a mock community) to determine the frequency of
57 mismatches between observed sequences and the most similar expected
58 sequences, e.g., as a measure of sequencing/method error. However, any
59 sequences may be provided as input to generate a report on pairwise
60 alignment quality against a set of reference sequences.
61
62 Parameters
63 ----------
64 query_sequences : FeatureData[Sequence]
65 Sequences to test for exclusion
66 reference_sequences : FeatureData[Sequence]
67 Reference sequences to align against feature sequences
68 show_alignments : Bool, optional
69 Option to plot pairwise alignments of query sequences and their top
70 hits.
71
72 Returns
73 -------
74 visualization : Visualization
75 ]]></help>
76 <macros>
77 <import>qiime_citation.xml</import>
78 </macros>
79 <expand macro="qiime_citation"/>
80 </tool>