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comparison qiime2/qiime_diversity_beta-rarefaction.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-rarefaction" name="qiime diversity beta-rarefaction" version="2019.4">
3 <description> - Beta diversity rarefaction</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-rarefaction
9
10 --i-table=$itable
11 --p-metric=$pmetric
12 --p-clustering-method=$pclusteringmethod
13 --p-sampling-depth="$psamplingdepth"
14
15 #if str($iphylogeny) != 'None':
16 --i-phylogeny=$iphylogeny
17 #end if
18
19 #if $piterations:
20 --p-iterations=$piterations
21 #end if
22
23 #if str($pcorrelationmethod) != 'None':
24 --p-correlation-method=$pcorrelationmethod
25 #end if
26
27 #if str($pcolorscheme) != 'None':
28 --p-color-scheme=$pcolorscheme
29 #end if
30
31 #def list_dict_to_string(list_dict):
32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
33 #for d in list_dict[1:]:
34 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
35 #end for
36 #return $file_list
37 #end def
38
39 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
40
41
42 --o-visualization=ovisualization
43 ;
44 cp mmetadatafile.qza $mmetadatafile;
45 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
46 && cp -r out/* '$ovisualization.files_path'
47 && mv '$ovisualization.files_path/index.html' '$ovisualization';
48 ]]></command>
49 <inputs>
50 <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"/>
51 <param label="--p-metric: " name="pmetric" optional="False" type="select">
52 <option value="kulsinski">kulsinski</option>
53 <option value="euclidean">euclidean</option>
54 <option value="wminkowski">wminkowski</option>
55 <option value="dice">dice</option>
56 <option value="correlation">correlation</option>
57 <option value="hamming">hamming</option>
58 <option value="canberra">canberra</option>
59 <option value="canberra_adkins">canberra_adkins</option>
60 <option value="rogerstanimoto">rogerstanimoto</option>
61 <option value="sqeuclidean">sqeuclidean</option>
62 <option value="cosine">cosine</option>
63 <option value="seuclidean">seuclidean</option>
64 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
65 <option value="sokalmichener">sokalmichener</option>
66 <option value="unweighted_unifrac">unweighted_unifrac</option>
67 <option value="cityblock">cityblock</option>
68 <option value="generalized_unifrac">generalized_unifrac</option>
69 <option value="weighted_unifrac">weighted_unifrac</option>
70 <option value="braycurtis">braycurtis</option>
71 <option value="jaccard">jaccard</option>
72 <option value="sokalsneath">sokalsneath</option>
73 <option value="aitchison">aitchison</option>
74 <option value="matching">matching</option>
75 <option value="chebyshev">chebyshev</option>
76 <option value="russellrao">russellrao</option>
77 <option value="yule">yule</option>
78 <option value="mahalanobis">mahalanobis</option>
79 </param>
80 <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
81 <option value="upgma">upgma</option>
82 <option value="nj">nj</option>
83 </param>
84 <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" min="1" value="" type="integer"/>
85 <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="True" type="data"/>
86 <param label="--p-iterations: INTEGER Number of times to rarefy the feature table at a Range(2, None) given sampling depth. [default: 10]" name="piterations" optional="True" type="integer" min="2" value="10"/>
87 <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
88 <option selected="True" value="None">Selection is Optional</option>
89 <option value="spearman">spearman</option>
90 <option value="pearson">pearson</option>
91 </param>
92 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
93 <option selected="True" value="None">Selection is Optional</option>
94 <option value="BrBG">BrBG</option>
95 <option value="BrBG_r">BrBG_r</option>
96 <option value="PRGn">PRGn</option>
97 <option value="PRGn_r">PRGn_r</option>
98 <option value="PiYG">PiYG</option>
99 <option value="PiYG_r">PiYG_r</option>
100 <option value="PuOr">PuOr</option>
101 <option value="PuOr_r">PuOr_r</option>
102 <option value="RdBu">RdBu</option>
103 <option value="RdBu_r">RdBu_r</option>
104 <option value="RdGy">RdGy</option>
105 <option value="RdGy_r">RdGy_r</option>
106 <option value="RdYlBu">RdYlBu</option>
107 <option value="RdYlBu_r">RdYlBu_r</option>
108 <option value="RdYlGn">RdYlGn</option>
109 <option value="RdYlGn_r">RdYlGn_r</option>
110 </param>
111
112 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
113 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
114 </repeat>
115
116 </inputs>
117 <outputs>
118 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
119 </outputs>
120 <help><![CDATA[
121 Beta diversity rarefaction
122 ##########################
123
124 Repeatedly rarefy a feature table to compare beta diversity results within
125 a given rarefaction depth. For a given beta diversity metric, this
126 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
127 by UPGMA or neighbor joining with support calculation, and a heatmap
128 showing the correlation between rarefaction trials of that beta diversity
129 metric.
130
131 Parameters
132 ----------
133 table : FeatureTable[Frequency]
134 Feature table upon which to perform beta diversity rarefaction
135 analyses.
136 metric : Str % Choices('generalized_unifrac', 'sokalmichener', 'matching', 'yule', 'weighted_normalized_unifrac', 'dice', 'russellrao', 'rogerstanimoto', 'mahalanobis', 'wminkowski', 'kulsinski', 'aitchison', 'seuclidean', 'correlation', 'sokalsneath', 'hamming', 'jaccard', 'unweighted_unifrac', 'weighted_unifrac', 'cosine', 'canberra', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'canberra_adkins', 'braycurtis')
137 The beta diversity metric to be computed.
138 clustering_method : Str % Choices('upgma', 'nj')
139 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
140 rarefaction trial will be used for the tree, and the remaining trials
141 are used to calculate the support of the internal nodes of that tree.
142 metadata : Metadata
143 The sample metadata used for the Emperor jackknifed PCoA plot.
144 sampling_depth : Int % Range(1, None)
145 The total frequency that each sample should be rarefied to prior to
146 computing the diversity metric.
147 iterations : Int % Range(2, None), optional
148 Number of times to rarefy the feature table at a given sampling depth.
149 phylogeny : Phylogeny[Rooted], optional
150 Phylogenetic tree containing tip identifiers that correspond to the
151 feature identifiers in the table. This tree can contain tip ids that
152 are not present in the table, but all feature ids in the table must be
153 present in this tree. [required for phylogenetic metrics]
154 correlation_method : Str % Choices('pearson', 'spearman'), optional
155 The Mantel correlation test to be applied when computing correlation
156 between beta diversity distance matrices.
157 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
158 The matplotlib color scheme to generate the heatmap with.
159
160 Returns
161 -------
162 visualization : Visualization
163 ]]></help>
164 <macros>
165 <import>qiime_citation.xml</import>
166 </macros>
167 <expand macro="qiime_citation"/>
168 </tool>