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comparison qiime2/qiime_vsearch_dereplicate-sequences.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_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2019.4">
3 <description> - Dereplicate sequences.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime vsearch dereplicate-sequences
9
10 --i-sequences=$isequences
11
12 #if $pderepprefix:
13 --p-derep-prefix
14 #end if
15
16 --o-dereplicated-table=odereplicatedtable
17 --o-dereplicated-sequences=odereplicatedsequences
18 ;
19 cp odereplicatedtable.qza $odereplicatedtable;
20 cp odereplicatedsequences.qza $odereplicatedsequences
21 ]]></command>
22 <inputs>
23 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data"/>
24 <param label="--p-derep-prefix: --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]" name="pderepprefix" selected="False" type="boolean"/>
25 </inputs>
26 <outputs>
27 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable"/>
28 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences"/>
29 </outputs>
30 <help><![CDATA[
31 Dereplicate sequences.
32 ######################
33
34 Dereplicate sequence data and create a feature table and feature
35 representative sequences. Feature identifiers in the resulting artifacts
36 will be the sha1 hash of the sequence defining each feature. If clustering
37 of features into OTUs is desired, the resulting artifacts can be passed to
38 the cluster_features_* methods in this plugin.
39
40 Parameters
41 ----------
42 sequences : SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
43 The sequences to be dereplicated.
44 derep_prefix : Bool, optional
45 Merge sequences with identical prefixes. If a sequence is identical to
46 the prefix of two or more longer sequences, it is clustered with the
47 shortest of them. If they are equally long, it is clustered with the
48 most abundant.
49
50 Returns
51 -------
52 dereplicated_table : FeatureTable[Frequency]
53 The table of dereplicated sequences.
54 dereplicated_sequences : FeatureData[Sequence]
55 The dereplicated sequences.
56 ]]></help>
57 <macros>
58 <import>qiime_citation.xml</import>
59 </macros>
60 <expand macro="qiime_citation"/>
61 </tool>