annotate qiime2/qiime_vsearch_cluster-features-closed-reference.xml @ 7:85b520815e85 draft

Uploaded
author florianbegusch
date Tue, 13 Aug 2019 07:53:59 -0400
parents a025a4a89e07
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-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Closed-reference 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-closed-reference
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9 --i-sequences=$isequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-reference-sequences=$ireferencesequences
5
a025a4a89e07 Uploaded
florianbegusch
parents: 0
diff changeset
12
a025a4a89e07 Uploaded
florianbegusch
parents: 0
diff changeset
13 #if str($ppercidentity):
a025a4a89e07 Uploaded
florianbegusch
parents: 0
diff changeset
14 --p-perc-identity="$ppercidentity"
a025a4a89e07 Uploaded
florianbegusch
parents: 0
diff changeset
15 #end if
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #if str($pstrand) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 --p-strand=$pstrand
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 #set $pthreads = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 #if str($pthreads):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 --p-threads="$pthreads"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 --o-clustered-table=oclusteredtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 --o-clustered-sequences=oclusteredsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 --o-unmatched-sequences=ounmatchedsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 cp oclusteredtable.qza $oclusteredtable;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 cp oclusteredsequences.qza $oclusteredsequences;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 cp ounmatchedsequences.qza $ounmatchedsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 <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
37 <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
38 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <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" type="float" value="" min="0" max="1" exclude_max="False" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <param label="--p-strand: " name="pstrand" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 <option value="plus">plus</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <option value="both">both</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <data format="qza" label="${tool.name} on ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 Open-reference clustering of features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 ######################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 Given a feature table and the associated feature sequences, cluster the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 features against a reference database based on user-specified percent
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 identity threshold of their sequences. Any sequences that don't match are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 then clustered de novo. This is not a general-purpose clustering method,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 but rather is intended to be used for clustering the results of quality-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 filtering/dereplication methods, such as DADA2, or for re-clustering a
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 FeatureTable at a lower percent identity than it was originally clustered
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 at. When a group of features in the input table are clustered into a single
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 feature, the frequency of that single feature in a given sample is the sum
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 of the frequencies of the features that were clustered in that sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 Feature identifiers will be inherited from the centroid feature of each
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 cluster. For features that match a reference sequence, the centroid feature
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 is that reference sequence, so its identifier will become the feature
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 identifier. The clustered_sequences result will contain feature
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 representative sequences that are derived from the sequences input for all
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 features in clustered_table. This will always be the most abundant sequence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 in the cluster. The new_reference_sequences result will contain the entire
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 reference database, plus feature representative sequences for any de novo
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 features. This is intended to be used as a reference database in subsequent
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 iterations of cluster_features_open_reference, if applicable. See the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 vsearch documentation for details on how sequence clustering is performed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 The sequences corresponding to the features in table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 The feature table to be clustered.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 reference_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 The sequences to use as cluster centroids.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 The percent identity at which clustering should be performed. This
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 parameter maps to vsearch's --id parameter.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 strand : Str % Choices('plus', 'both'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 Search plus (i.e., forward) or both (i.e., forward and reverse
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 complement) strands.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 clustered_table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 The table following clustering of features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 clustered_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 Sequences representing clustered features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 new_reference_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 The new reference sequences. This can be used for subsequent runs of
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 open-reference clustering for consistent definitions of features across
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 open-reference feature tables.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 </tool>