annotate qiime2/qiime_diversity_pcoa.xml @ 2:51025741f326 draft

Uploaded
author florianbegusch
date Thu, 18 Jul 2019 12:19:15 -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_diversity_pcoa" name="qiime diversity pcoa" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Principal Coordinate Analysis</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 diversity pcoa
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-distance-matrix=$idistancematrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 #if str($pnumberofdimensions):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --p-number-of-dimensions="$pnumberofdimensions"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --o-pcoa=opcoa
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 cp opcoa.qza $opcoa
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix The distance matrix on which PCoA should be computed. [required]" name="idistancematrix" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <param label="--p-number-of-dimensions: INTEGER Range(1, None) Dimensions to reduce the distance matrix to. This number determines how many eigenvectors and eigenvalues are returned,and influences the choice of algorithm used to compute them. By default, uses the default eigendecomposition method, SciPy's eigh, which computes all eigenvectors and eigenvalues in an exact manner. For very large matrices, this is expected to be slow. If a value is specified for this parameter, then the fast, heuristic eigendecomposition algorithm fsvd is used, which only computes and returns the number of dimensions specified, but suffers some degree of accuracy loss, the magnitude of which varies across different datasets. [optional]" name="pnumberofdimensions" optional="True" min="1" type="integer"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <data format="qza" label="${tool.name} on ${on_string}: pcoa.qza" name="opcoa"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 Principal Coordinate Analysis
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 #############################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 Apply principal coordinate analysis.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 distance_matrix : DistanceMatrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 The distance matrix on which PCoA should be computed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 number_of_dimensions : Int % Range(1, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 Dimensions to reduce the distance matrix to. This number determines how
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 many eigenvectors and eigenvalues are returned,and influences the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 choice of algorithm used to compute them. By default, uses the default
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 eigendecomposition method, SciPy's eigh, which computes all
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 eigenvectors and eigenvalues in an exact manner. For very large
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 matrices, this is expected to be slow. If a value is specified for this
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 parameter, then the fast, heuristic eigendecomposition algorithm fsvd
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 is used, which only computes and returns the number of dimensions
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 specified, but suffers some degree of accuracy loss, the magnitude of
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 which varies across different datasets.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 pcoa : PCoAResults
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 The resulting PCoA matrix.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 </tool>