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comparison qiime2/qiime_diversity_beta-correlation.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" version="2019.4">
3 <description> - Beta diversity correlation</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-correlation
9
10 --i-distance-matrix=$idistancematrix
11 --m-metadata-column="$mmetadatacolumn"
12
13 #if str($pmethod) != 'None':
14 --p-method=$pmethod
15 #end if
16
17 #if $ppermutations:
18 --p-permutations=$ppermutations
19 #end if
20
21 #if $pintersectids:
22 --p-intersect-ids
23 #end if
24
25 #if str($plabel1):
26 --p-label1="$plabel1"
27 #end if
28
29 #if str($plabel2):
30 --p-label2="$plabel2"
31 #end if
32
33 #if $input_files_mmetadatafile:
34 #def list_dict_to_string(list_dict):
35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
36 #for d in list_dict[1:]:
37 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
38 #end for
39 #return $file_list
40 #end def
41 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
42 #end if
43
44 --o-metadata-distance-matrix=ometadatadistancematrix
45 --o-mantel-scatter-visualization=omantelscattervisualization
46 ;
47 cp ometadatadistancematrix.qza $ometadatadistancematrix;
48 qiime tools export --input-path omantelscattervisualization.qzv --output-path out && mkdir -p '$omantelscattervisualization.files_path'
49 && cp -r out/* '$omantelscattervisualization.files_path'
50 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
51 ]]></command>
52 <inputs>
53 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
54 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column from which to compute pairwise Euclidean distances [required]" name="mmetadatacolumn" optional="False" type="text"/>
55 <param label="--p-method: " name="pmethod" optional="True" type="select">
56 <option selected="True" value="None">Selection is Optional</option>
57 <option value="spearman">spearman</option>
58 <option value="pearson">pearson</option>
59 </param>
60 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
61 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
62 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="'Metadata'"/>
63 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="'Distance Matrix'"/>
64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
65 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
66 </repeat>
67 </inputs>
68 <outputs>
69 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
70 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
71 </outputs>
72 <help><![CDATA[
73 Beta diversity correlation
74 ##########################
75
76 Create a distance matrix from a numeric metadata column and apply a two-
77 sided Mantel test to identify correlation between two distance matrices.
78 Actions used internally: `distance-matrix` from q2-metadata and `mantel`
79 from q2-diversity.
80
81 Parameters
82 ----------
83 metadata : MetadataColumn[Numeric]
84 Numeric metadata column from which to compute pairwise Euclidean
85 distances
86 distance_matrix : DistanceMatrix
87 Matrix of distances between pairs of samples.
88 method : Str % Choices('spearman', 'pearson'), optional
89 The correlation test to be applied in the Mantel test.
90 permutations : Int % Range(0, None), optional
91 The number of permutations to be run when computing p-values. Supplying
92 a value of zero will disable permutation testing and p-values will not
93 be calculated (this results in *much* quicker execution time if
94 p-values are not desired).
95 intersect_ids : Bool, optional
96 If supplied, IDs that are not found in both distance matrices will be
97 discarded before applying the Mantel test. Default behavior is to error
98 on any mismatched IDs.
99 label1 : Str, optional
100 Label for `distance_matrix` in the output visualization.
101 label2 : Str, optional
102 Label for `metadata_distance_matrix` in the output visualization.
103
104 Returns
105 -------
106 metadata_distance_matrix : DistanceMatrix
107 The Distance Matrix produced from the metadata column and used in the
108 mantel test
109 mantel_scatter_visualization : Visualization
110 Scatter plot rendering of the manteltest results
111 ]]></help>
112 <macros>
113 <import>qiime_citation.xml</import>
114 </macros>
115 <expand macro="qiime_citation"/>
116 </tool>