comparison qiime2/qiime_diversity_beta-rarefaction.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2018.4">
3 <description> - Beta diversity rarefaction</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-rarefaction --i-table=$itable
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-clustering-method=$pclusteringmethod --p-metric=$pmetric --p-sampling-depth="$psamplingdepth"
19
20 #if str($pcorrelationmethod) != 'None':
21 --p-correlation-method=$pcorrelationmethod
22 #end if
23
24 #if str($pcolorscheme) != 'None':
25 --p-color-scheme=$pcolorscheme
26 #end if
27
28 --o-visualization=ovisualization
29
30 #if str($cmdconfig) != 'None':
31 --cmd-config=$cmdconfig
32 #end if
33
34 #if str($iphylogeny) != 'None':
35 --i-phylogeny=$iphylogeny
36 #end if
37
38 #if $piterations:
39 --p-iterations=$piterations
40 #end if
41 ;
42 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization';
45 ]]></command>
46 <inputs>
47 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses. [required]" name="itable" optional="False" type="data"/>
48 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Phylogenetic tree containing tip identifiers that 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="True" type="data"/>
49
50 <param label="--p-metric: The beta diversity metric to be computed.
51 [required]" name="pmetric" optional="False" type="select">
52 <option value="hamming">hamming</option>
53 <option value="sqeuclidean">sqeuclidean</option>
54 <option value="cityblock">cityblock</option>
55 <option value="sokalmichener">sokalmichener</option>
56 <option value="braycurtis">braycurtis</option>
57 <option value="cosine">cosine</option>
58 <option value="euclidean">euclidean</option>
59 <option value="rogerstanimoto">rogerstanimoto</option>
60 <option value="weighted_unifrac">weighted_unifrac</option>
61 <option value="canberra">canberra</option>
62 <option value="seuclidean">seuclidean</option>
63 <option value="correlation">correlation</option>
64 <option value="unweighted_unifrac">unweighted_unifrac</option>
65 <option value="sokalsneath">sokalsneath</option>
66 <option value="chebyshev">chebyshev</option>
67 <option value="mahalanobis">mahalanobis</option>
68 <option value="matching">matching</option>
69 <option value="kulsinski">kulsinski</option>
70 <option value="yule">yule</option>
71 <option value="dice">dice</option>
72 <option value="russellrao">russellrao</option>
73 <option value="wminkowski">wminkowski</option>
74 <option value="jaccard">jaccard</option>
75 </param>
76 <param label="--p-clustering-method: Samples can be clustered with neighbor
77 joining or UPGMA. An arbitrary rarefaction
78 trial will be used for the tree, and the
79 remaining trials are used to calculate the
80 support of the internal nodes of that tree.
81 [required]" name="pclusteringmethod" optional="False" type="select">
82 <option value="upgma">upgma</option>
83 <option value="nj">nj</option>
84 </param>
85
86 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
87 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
88 </repeat>
89
90 <param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]" name="psamplingdepth" optional="False" type="text"/>
91 <param label="--p-iterations: Number of times to rarefy the feature table at a given sampling depth. [default: 10]" name="piterations" optional="True" type="integer" value="10"/>
92
93 <param label="--p-correlation-method: The Mantel correlation test to be applied
94 when computing correlation between beta
95 diversity distance matrices. [default:
96 spearman]" name="pcorrelationmethod" optional="True" type="select">
97 <option selected="True" value="spearman">spearman</option>
98 <option value="pearson">pearson</option>
99 </param>
100
101 <param label="--p-color-scheme: The matplotlib color scheme to generate the
102 heatmap with. [default: BrBG]" name="pcolorscheme" optional="True" type="select">
103 <option value="PiYG">PiYG</option>
104 <option value="RdYlGn_r">RdYlGn_r</option>
105 <option value="RdYlBu_r">RdYlBu_r</option>
106 <option value="RdYlGn">RdYlGn</option>
107 <option value="BrBG_r">BrBG_r</option>
108 <option value="RdYlBu">RdYlBu</option>
109 <option value="RdGy">RdGy</option>
110 <option value="PuOr">PuOr</option>
111 <option value="RdBu_r">RdBu_r</option>
112 <option value="RdGy_r">RdGy_r</option>
113 <option value="PiYG_r">PiYG_r</option>
114 <option value="RdBu">RdBu</option>
115 <option value="PuOr_r">PuOr_r</option>
116 <option value="PRGn">PRGn</option>
117 <option selected="True" value="BrBG">BrBG</option>
118 <option value="PRGn_r">PRGn_r</option>
119 </param>
120
121 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
122 </inputs>
123 <outputs>
124 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
125 </outputs>
126 <help><![CDATA[
127 Beta diversity rarefaction
128 --------------------------
129
130 Repeatedly rarefy a feature table to compare beta diversity results within
131 a given rarefaction depth. For a given beta diversity metric, this
132 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
133 by UPGMA or neighbor joining with support calculation, and a heatmap
134 showing the correlation between rarefaction trials of that beta diversity
135 metric.
136
137 Parameters
138 ----------
139 table : FeatureTable[Frequency]
140 Feature table upon which to perform beta diversity rarefaction
141 analyses.
142 phylogeny : Phylogeny[Rooted], optional
143 Phylogenetic tree containing tip identifiers that correspond to the
144 feature identifiers in the table. This tree can contain tip ids that
145 are not present in the table, but all feature ids in the table must be
146 present in this tree. [required for phylogenetic metrics]
147 metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'unweighted_unifrac', 'weighted_unifrac', 'wminkowski', 'yule'})
148 The beta diversity metric to be computed.
149 clustering_method : Str % Choices({'nj', 'upgma'})
150 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
151 rarefaction trial will be used for the tree, and the remaining trials
152 are used to calculate the support of the internal nodes of that tree.
153 metadata : Metadata
154 The sample metadata used for the Emperor jackknifed PCoA plot.
155 sampling_depth : Int % Range(1, None)
156 The total frequency that each sample should be rarefied to prior to
157 computing the diversity metric.
158 iterations : Int % Range(2, None), optional
159 Number of times to rarefy the feature table at a given sampling depth.
160 correlation_method : Str % Choices({'pearson', 'spearman'}), optional
161 The Mantel correlation test to be applied when computing correlation
162 between beta diversity distance matrices.
163 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
164 The matplotlib color scheme to generate the heatmap with.
165
166 Returns
167 -------
168 visualization : Visualization
169 \
170 ]]>
171 </help>
172 <macros>
173 <import>qiime_citation.xml</import>
174 </macros>
175 <expand macro="qiime_citation" />
176 </tool>