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comparison qiime2-2020.8/qiime_diversity_beta-rarefaction.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction"
3 version="2020.8">
4 <description>Beta diversity rarefaction</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity beta-rarefaction
10
11 --i-table=$itable
12
13 #if str($iphylogeny) != 'None':
14 --i-phylogeny=$iphylogeny
15 #end if
16
17 --p-metric=$pmetric
18
19 --p-clustering-method=$pclusteringmethod
20 # if $input_files_mmetadatafile:
21 # def list_dict_to_string(list_dict):
22 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
23 # for d in list_dict[1:]:
24 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
25 # end for
26 # return $file_list
27 # end def
28 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
29 # end if
30
31 --p-sampling-depth=$psamplingdepth
32
33 --p-iterations=$piterations
34
35 #if str($pcorrelationmethod) != 'None':
36 --p-correlation-method=$pcorrelationmethod
37 #end if
38
39 #if str($pcolorscheme) != 'None':
40 --p-color-scheme=$pcolorscheme
41 #end if
42
43 --o-visualization=ovisualization
44
45 #if str($examples) != 'None':
46 --examples=$examples
47 #end if
48
49 ;
50 cp odistancematrix.qza $odistancematrix
51
52 ;
53 qiime tools export ovisualization.qzv --output-path out
54 && mkdir -p '$ovisualization.files_path'
55 && cp -r out/* '$ovisualization.files_path'
56 && mv '$ovisualization.files_path/index.html' '$ovisualization'
57
58 ]]></command>
59 <inputs>
60 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses. [required]" name="itable" optional="False" type="data" />
61 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]" name="iphylogeny" optional="False" type="data" />
62 <param label="--p-metric: " name="pmetric" optional="False" type="select">
63 <option value="braycurtis">braycurtis</option>
64 <option value="euclidean">euclidean</option>
65 <option value="cityblock">cityblock</option>
66 <option value="cosine">cosine</option>
67 <option value="minkowski">minkowski</option>
68 <option value="matching">matching</option>
69 <option value="correlation">correlation</option>
70 <option value="russellrao">russellrao</option>
71 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
72 <option value="sokalsneath">sokalsneath</option>
73 <option value="seuclidean">seuclidean</option>
74 <option value="canberra">canberra</option>
75 <option value="sokalmichener">sokalmichener</option>
76 <option value="kulsinski">kulsinski</option>
77 <option value="jensenshannon">jensenshannon</option>
78 <option value="weighted_unifrac">weighted_unifrac</option>
79 <option value="jaccard">jaccard</option>
80 <option value="hamming">hamming</option>
81 <option value="chebyshev">chebyshev</option>
82 <option value="generalized_unifrac">generalized_unifrac</option>
83 <option value="yule">yule</option>
84 <option value="dice">dice</option>
85 <option value="sqeuclidean">sqeuclidean</option>
86 <option value="aitchison">aitchison</option>
87 <option value="canberra_adkins">canberra_adkins</option>
88 <option value="unweighted_unifrac">unweighted_unifrac</option>
89 <option value="rogerstanimoto">rogerstanimoto</option>
90 </param>
91 <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
92 <option value="upgma">upgma</option>
93 <option value="nj">nj</option>
94 </param>
95 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
96 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata used for the Emperor jackknifed will be merged) PCoA plot. [required]" name="additional_input" optional="False" type="data" />
97 </repeat>
98 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]" name="psamplingdepth" optional="False" type="text" />
99 <param label="--p-iterations: INTEGER Number of times to rarefy the feature table at a Range(2, None) given sampling depth. [default: 10]" min="2" name="piterations" optional="True" type="integer" value="10" />
100 <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
101 <option selected="True" value="None">Selection is Optional</option>
102 <option value="pearson">pearson</option>
103 <option value="spearman">spearman</option>
104 </param>
105 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
106 <option selected="True" value="None">Selection is Optional</option>
107 <option value="BrBG">BrBG</option>
108 <option value="BrBG_r">BrBG_r</option>
109 <option value="PRGn">PRGn</option>
110 <option value="PRGn_r">PRGn_r</option>
111 <option value="PiYG">PiYG</option>
112 <option value="PiYG_r">PiYG_r</option>
113 <option value="PuOr">PuOr</option>
114 <option value="PuOr_r">PuOr_r</option>
115 <option value="RdBu">RdBu</option>
116 <option value="RdBu_r">RdBu_r</option>
117 <option value="RdGy">RdGy</option>
118 <option value="RdGy_r">RdGy_r</option>
119 <option value="RdYlBu">RdYlBu</option>
120 <option value="RdYlBu_r">RdYlBu_r</option>
121 <option value="RdYlGn">RdYlGn</option>
122 <option value="RdYlGn_r">RdYlGn_r</option>
123 </param>
124 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
125
126 </inputs>
127
128 <outputs>
129 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
130
131 </outputs>
132
133 <help><![CDATA[
134 Beta diversity rarefaction
135 ###############################################################
136
137 Repeatedly rarefy a feature table to compare beta diversity results within
138 a given rarefaction depth. For a given beta diversity metric, this
139 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
140 by UPGMA or neighbor joining with support calculation, and a heatmap
141 showing the correlation between rarefaction trials of that beta diversity
142 metric.
143
144 Parameters
145 ----------
146 table : FeatureTable[Frequency]
147 Feature table upon which to perform beta diversity rarefaction
148 analyses.
149 metric : Str % Choices('yule', 'weighted_normalized_unifrac', 'cityblock', 'weighted_unifrac', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'generalized_unifrac', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'unweighted_unifrac', 'chebyshev', 'jensenshannon')
150 The beta diversity metric to be computed.
151 clustering_method : Str % Choices('upgma', 'nj')
152 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
153 rarefaction trial will be used for the tree, and the remaining trials
154 are used to calculate the support of the internal nodes of that tree.
155 metadata : Metadata
156 The sample metadata used for the Emperor jackknifed PCoA plot.
157 sampling_depth : Int % Range(1, None)
158 The total frequency that each sample should be rarefied to prior to
159 computing the diversity metric.
160 iterations : Int % Range(2, None), optional
161 Number of times to rarefy the feature table at a given sampling depth.
162 phylogeny : Phylogeny[Rooted], optional
163 Phylogenetic tree containing tip identifiers that correspond to the
164 feature identifiers in the table. This tree can contain tip ids that
165 are not present in the table, but all feature ids in the table must be
166 present in this tree. [required for phylogenetic metrics]
167 correlation_method : Str % Choices('spearman', 'pearson'), optional
168 The Mantel correlation test to be applied when computing correlation
169 between beta diversity distance matrices.
170 color_scheme : Str % Choices('BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r'), optional
171 The matplotlib color scheme to generate the heatmap with.
172
173 Returns
174 -------
175 visualization : Visualization
176 ]]></help>
177 <macros>
178 <import>qiime_citation.xml</import>
179 </macros>
180 <expand macro="qiime_citation"/>
181 </tool>