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comparison qiime2-2020.8/qiime_vsearch_dereplicate-sequences.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences"
3 version="2020.8">
4 <description>Dereplicate sequences.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime vsearch dereplicate-sequences
10
11 --i-sequences=$isequences
12
13 #if $pderepprefix:
14 --p-derep-prefix
15 #end if
16
17 --o-dereplicated-table=odereplicatedtable
18
19 --o-dereplicated-sequences=odereplicatedsequences
20
21 #if str($examples) != 'None':
22 --examples=$examples
23 #end if
24
25 ;
26 cp odereplicatedsequences.qza $odereplicatedsequences
27
28 ]]></command>
29 <inputs>
30 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data" />
31 <param label="--p-derep-prefix: --p-derep-prefix: / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]" name="pderepprefix" selected="False" type="boolean" />
32 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
33
34 </inputs>
35
36 <outputs>
37 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable" />
38 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences" />
39
40 </outputs>
41
42 <help><![CDATA[
43 Dereplicate sequences.
44 ###############################################################
45
46 Dereplicate sequence data and create a feature table and feature
47 representative sequences. Feature identifiers in the resulting artifacts
48 will be the sha1 hash of the sequence defining each feature. If clustering
49 of features into OTUs is desired, the resulting artifacts can be passed to
50 the cluster_features_* methods in this plugin.
51
52 Parameters
53 ----------
54 sequences : SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
55 The sequences to be dereplicated.
56 derep_prefix : Bool, optional
57 Merge sequences with identical prefixes. If a sequence is identical to
58 the prefix of two or more longer sequences, it is clustered with the
59 shortest of them. If they are equally long, it is clustered with the
60 most abundant.
61
62 Returns
63 -------
64 dereplicated_table : FeatureTable[Frequency]
65 The table of dereplicated sequences.
66 dereplicated_sequences : FeatureData[Sequence]
67 The dereplicated sequences.
68 ]]></help>
69 <macros>
70 <import>qiime_citation.xml</import>
71 </macros>
72 <expand macro="qiime_citation"/>
73 </tool>