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comparison qiime2/qiime_diversity-lib_bray-curtis.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
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>