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comparison qiime2/qiime_diversity-lib_jaccard.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity-lib_jaccard" name="qiime diversity-lib jaccard"
3 version="2020.8">
4 <description>Jaccard Distance</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity-lib jaccard
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 $odistancematrix
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which Jaccard distance should be computed. [required]" name="itable" optional="False" type="data" />
29 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
30 <option selected="True" value="None">Selection is Optional</option>
31 <option value="Int % Range(1">Int % Range(1</option>
32 <option value="None">None</option>
33 </param>
34 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
35
36 </inputs>
37
38 <outputs>
39 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
40
41 </outputs>
42
43 <help><![CDATA[
44 Jaccard Distance
45 ###############################################################
46
47 Compute Jaccard distance for each sample in a feature table. Jaccard is
48 calculated usingpresence/absence data. Data of type FeatureTable[Frequency
49 | Relative Frequency] is reducedto presence/absence prior to calculation.
50
51 Parameters
52 ----------
53 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
54 The feature table containing the samples for which Jaccard distance
55 should be computed.
56 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
57 The number of concurrent jobs to use in performing this calculation.
58 May not exceed the number of available physical cores. If n_jobs =
59 'auto', one job will be launched for each identified CPU core on the
60 host.
61
62 Returns
63 -------
64 distance_matrix : DistanceMatrix
65 Distance matrix for Jaccard index
66 ]]></help>
67 <macros>
68 <import>qiime_citation.xml</import>
69 </macros>
70 <expand macro="qiime_citation"/>
71 </tool>