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comparison qiime2/qiime_quality-control_evaluate-seqs.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2019.4">
3 <description> - Compare query (observed) vs. reference (expected) sequences.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime quality-control evaluate-seqs
9
10 --i-query-sequences=$iquerysequences
11 --i-reference-sequences=$ireferencesequences
12
13 --o-visualization=ovisualization
14 ;
15 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
16 && cp -r out/* '$ovisualization.files_path'
17 && mv '$ovisualization.files_path/index.html' '$ovisualization';
18 ]]></command>
19 <inputs>
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"/>
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"/>
22 </inputs>
23 <outputs>
24 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
25 </outputs>
26 <help><![CDATA[
27 Compare query (observed) vs. reference (expected) sequences.
28 ############################################################
29
30 This action aligns a set of query (e.g., observed) sequences against a set
31 of reference (e.g., expected) sequences to evaluate the quality of
32 alignment. The intended use is to align observed sequences against expected
33 sequences (e.g., from a mock community) to determine the frequency of
34 mismatches between observed sequences and the most similar expected
35 sequences, e.g., as a measure of sequencing/method error. However, any
36 sequences may be provided as input to generate a report on pairwise
37 alignment quality against a set of reference sequences.
38
39 Parameters
40 ----------
41 query_sequences : FeatureData[Sequence]
42 Sequences to test for exclusion
43 reference_sequences : FeatureData[Sequence]
44 Reference sequences to align against feature sequences
45 show_alignments : Bool, optional
46 Option to plot pairwise alignments of query sequences and their top
47 hits.
48
49 Returns
50 -------
51 visualization : Visualization
52 ]]></help>
53 <macros>
54 <import>qiime_citation.xml</import>
55 </macros>
56 <expand macro="qiime_citation"/>
57 </tool>