|
14
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity-lib_bray-curtis" name="qiime diversity-lib bray-curtis"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Bray-Curtis Dissimilarity</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime diversity-lib bray-curtis
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
|
12
|
|
|
13 #if str($pnjobs) != 'None':
|
|
|
14 --p-n-jobs=$pnjobs
|
|
|
15 #end if
|
|
|
16
|
|
|
17 --o-distance-matrix=odistancematrix
|
|
|
18
|
|
|
19 #if str($examples) != 'None':
|
|
|
20 --examples=$examples
|
|
|
21 #end if
|
|
|
22
|
|
|
23 ;
|
|
|
24 cp odistancematrix.qza $odistancematrix
|
|
|
25
|
|
|
26 ]]></command>
|
|
|
27 <inputs>
|
|
|
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed. [required]" name="itable" optional="False" type="data" />
|
|
|
29 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
|
|
|
30 <option selected="True" value="None">Selection is Optional</option>
|
|
|
31 <option value="Int % Range(1">Int % Range(1</option>
|
|
|
32 <option value="None">None</option>
|
|
|
33 </param>
|
|
|
34 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
35
|
|
|
36 </inputs>
|
|
|
37
|
|
|
38 <outputs>
|
|
|
39 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
|
|
|
40
|
|
|
41 </outputs>
|
|
|
42
|
|
|
43 <help><![CDATA[
|
|
|
44 Bray-Curtis Dissimilarity
|
|
|
45 ###############################################################
|
|
|
46
|
|
|
47 Compute Bray-Curtis dissimilarity for each sample in a feature table. Note:
|
|
|
48 Frequency and relative frequency data produce different results unless
|
|
|
49 overall sample sizes are identical. Please consider the impact on your
|
|
|
50 results if you use Bray-Curtis with count data that has not been adjusted
|
|
|
51 (normalized).
|
|
|
52
|
|
|
53 Parameters
|
|
|
54 ----------
|
|
|
55 table : FeatureTable[Frequency]
|
|
|
56 The feature table containing the samples for which Bray-Curtis
|
|
|
57 dissimilarity should be computed.
|
|
|
58 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
|
|
|
59 The number of concurrent jobs to use in performing this calculation.
|
|
|
60 May not exceed the number of available physical cores. If n_jobs =
|
|
|
61 'auto', one job will be launched for each identified CPU core on the
|
|
|
62 host.
|
|
|
63
|
|
|
64 Returns
|
|
|
65 -------
|
|
|
66 distance_matrix : DistanceMatrix
|
|
|
67 Distance matrix for Bray-Curtis dissimilarity
|
|
|
68 ]]></help>
|
|
|
69 <macros>
|
|
|
70 <import>qiime_citation.xml</import>
|
|
|
71 </macros>
|
|
|
72 <expand macro="qiime_citation"/>
|
|
|
73 </tool> |
