annotate qiime2/qiime_vsearch_cluster-features-de-novo.xml @ 1:255f48db74f8 draft

Hotfix
author florianbegusch
date Wed, 17 Jul 2019 03:26:16 -0400
parents 370e0b6e9826
children f190567fe3f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - De novo clustering of features.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime vsearch cluster-features-de-novo
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-sequences=$isequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-perc-identity="$ppercidentity"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #set $pthreads = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #if str($pthreads):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --p-threads="$pthreads"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 --o-clustered-table=oclusteredtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 --o-clustered-sequences=oclusteredsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 cp oclusteredtable.qza $oclusteredtable;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 cp oclusteredsequences.qza $oclusteredsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]" name="ppercidentity" optional="False" min="0" max="1" value="" exclude_min="True" exclude_max="False" type="float"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 De novo clustering of features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 ###############################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 Given a feature table and the associated feature sequences, cluster the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 features based on user-specified percent identity threshold of their
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 sequences. This is not a general-purpose de novo clustering method, but
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 rather is intended to be used for clustering the results of quality-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 filtering/dereplication methods, such as DADA2, or for re-clustering a
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 FeatureTable at a lower percent identity than it was originally clustered
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 at. When a group of features in the input table are clustered into a single
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 feature, the frequency of that single feature in a given sample is the sum
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 of the frequencies of the features that were clustered in that sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 Feature identifiers and sequences will be inherited from the centroid
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 feature of each cluster. See the vsearch documentation for details on how
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 sequence clustering is performed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 The sequences corresponding to the features in table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 The feature table to be clustered.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 The percent identity at which clustering should be performed. This
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 parameter maps to vsearch's --id parameter.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 clustered_table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 The table following clustering of features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 clustered_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 Sequences representing clustered features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 </tool>