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comparison qiime2/qiime_vsearch_dereplicate-sequences.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2018.4">
3 <description> - Dereplicate sequences.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime vsearch dereplicate-sequences --i-sequences=$isequences --o-dereplicated-sequences=odereplicatedsequences
10
11 #if str($cmdconfig) != 'None':
12 --cmd-config=$cmdconfig
13 #end if
14 --o-dereplicated-table=odereplicatedtable;
15
16 cp odereplicatedsequences.qza $odereplicatedsequences;
17 cp odereplicatedtable.qza $odereplicatedtable;
18 ]]>
19 </command>
20 <inputs>
21 <param format="qza,no_unzip.zip" label="--i-sequences: SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data"/>
22
23 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
24 </inputs>
25 <outputs>
26 <data format="qza" label="${tool.name} on ${on_string}: dereplicated-sequences.qza" name="odereplicatedsequences"/>
27 <data format="qza" label="${tool.name} on ${on_string}: dereplicated-table.qza" name="odereplicatedtable"/>
28 </outputs>
29 <help>
30 <![CDATA[
31 Dereplicate sequences.
32 -----------------------
33
34 Dereplicate sequence data and create a feature table and feature
35 representative sequences. Feature identfiers 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[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences]
43 The sequences to be dereplicated.
44
45 Returns
46 -------
47 dereplicated_table : FeatureTable[Frequency]
48 The table of dereplicated sequences.
49 dereplicated_sequences : FeatureData[Sequence]
50 The dereplicated sequences.
51 ]]>
52 </help>
53 <macros>
54 <import>qiime_citation.xml</import>
55 </macros>
56 <expand macro="qiime_citation" />
57 </tool>