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comparison qiime2/qiime_diversity_beta-rarefaction.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2019.7"> 2 <tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction"
3 <description> - Beta diversity rarefaction</description> 3 version="2020.8">
4 <requirements> 4 <description>Beta diversity rarefaction</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime diversity beta-rarefaction 9 qiime diversity beta-rarefaction
9 10
10 --i-table=$itable 11 --i-table=$itable
11 12
13 #if str($iphylogeny) != 'None':
14 --i-phylogeny=$iphylogeny
15 #end if
16
12 --p-metric=$pmetric 17 --p-metric=$pmetric
13 18
14 --p-clustering-method=$pclusteringmethod 19 --p-clustering-method=$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($input_files_mmetadatafile)
29 # end if
15 30
16 #if str($psamplingdepth): 31 --p-sampling-depth=$psamplingdepth
17 --p-sampling-depth="$psamplingdepth"
18 #end if
19 32
20 #if str($iphylogeny) != 'None': 33 --p-iterations=$piterations
21 --i-phylogeny=$iphylogeny
22 #end if
23
24 #if str($piterations):
25 --p-iterations=$piterations
26 #end if
27 34
28 #if str($pcorrelationmethod) != 'None': 35 #if str($pcorrelationmethod) != 'None':
29 --p-correlation-method=$pcorrelationmethod 36 --p-correlation-method=$pcorrelationmethod
30 #end if 37 #end if
31 38
32 #if str($pcolorscheme) != 'None': 39 #if str($pcolorscheme) != 'None':
33 --p-color-scheme=$pcolorscheme 40 --p-color-scheme=$pcolorscheme
34 #end if
35
36 #if $input_files_mmetadatafile:
37 #def list_dict_to_string(list_dict):
38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
39 #for d in list_dict[1:]:
40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
41 #end for
42 #return $file_list
43 #end def
44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
45 #end if 41 #end if
46 42
47 --o-visualization=ovisualization 43 --o-visualization=ovisualization
44
45 #if str($examples) != 'None':
46 --examples=$examples
47 #end if
48
48 ; 49 ;
49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 50 cp odistancematrix.qza $odistancematrix
51
52 ;
53 qiime tools export ovisualization.qzv --output-path out
54 && mkdir -p '$ovisualization.files_path'
50 && cp -r out/* '$ovisualization.files_path' 55 && cp -r out/* '$ovisualization.files_path'
51 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 56 && mv '$ovisualization.files_path/index.html' '$ovisualization'
52 ]]></command>
53 <inputs>
54 <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"/>
55 <param label="--p-metric: " name="pmetric" optional="False" type="select">
56 <option value="kulsinski">kulsinski</option>
57 <option value="euclidean">euclidean</option>
58 <option value="wminkowski">wminkowski</option>
59 <option value="dice">dice</option>
60 <option value="correlation">correlation</option>
61 <option value="hamming">hamming</option>
62 <option value="canberra">canberra</option>
63 <option value="canberra_adkins">canberra_adkins</option>
64 <option value="rogerstanimoto">rogerstanimoto</option>
65 <option value="sqeuclidean">sqeuclidean</option>
66 <option value="cosine">cosine</option>
67 <option value="seuclidean">seuclidean</option>
68 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
69 <option value="sokalmichener">sokalmichener</option>
70 <option value="unweighted_unifrac">unweighted_unifrac</option>
71 <option value="cityblock">cityblock</option>
72 <option value="generalized_unifrac">generalized_unifrac</option>
73 <option value="weighted_unifrac">weighted_unifrac</option>
74 <option value="braycurtis">braycurtis</option>
75 <option value="jaccard">jaccard</option>
76 <option value="sokalsneath">sokalsneath</option>
77 <option value="aitchison">aitchison</option>
78 <option value="matching">matching</option>
79 <option value="chebyshev">chebyshev</option>
80 <option value="russellrao">russellrao</option>
81 <option value="yule">yule</option>
82 <option value="mahalanobis">mahalanobis</option>
83 </param>
84 <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
85 <option value="upgma">upgma</option>
86 <option value="nj">nj</option>
87 </param>
88 <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"/>
89 <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"/>
90 <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"/>
91 <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
92 <option selected="True" value="None">Selection is Optional</option>
93 <option value="spearman">spearman</option>
94 <option value="pearson">pearson</option>
95 </param>
96 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
97 <option selected="True" value="None">Selection is Optional</option>
98 <option value="BrBG">BrBG</option>
99 <option value="BrBG_r">BrBG_r</option>
100 <option value="PRGn">PRGn</option>
101 <option value="PRGn_r">PRGn_r</option>
102 <option value="PiYG">PiYG</option>
103 <option value="PiYG_r">PiYG_r</option>
104 <option value="PuOr">PuOr</option>
105 <option value="PuOr_r">PuOr_r</option>
106 <option value="RdBu">RdBu</option>
107 <option value="RdBu_r">RdBu_r</option>
108 <option value="RdGy">RdGy</option>
109 <option value="RdGy_r">RdGy_r</option>
110 <option value="RdYlBu">RdYlBu</option>
111 <option value="RdYlBu_r">RdYlBu_r</option>
112 <option value="RdYlGn">RdYlGn</option>
113 <option value="RdYlGn_r">RdYlGn_r</option>
114 </param>
115 57
116 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> 58 ]]></command>
117 <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" /> 59 <inputs>
118 </repeat> 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>
119 127
120 </inputs> 128 <outputs>
121 <outputs> 129 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
122 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 130
123 </outputs> 131 </outputs>
124 <help><![CDATA[ 132
133 <help><![CDATA[
125 Beta diversity rarefaction 134 Beta diversity rarefaction
126 ########################## 135 ###############################################################
127 136
128 Repeatedly rarefy a feature table to compare beta diversity results within 137 Repeatedly rarefy a feature table to compare beta diversity results within
129 a given rarefaction depth. For a given beta diversity metric, this 138 a given rarefaction depth. For a given beta diversity metric, this
130 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered 139 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
131 by UPGMA or neighbor joining with support calculation, and a heatmap 140 by UPGMA or neighbor joining with support calculation, and a heatmap
135 Parameters 144 Parameters
136 ---------- 145 ----------
137 table : FeatureTable[Frequency] 146 table : FeatureTable[Frequency]
138 Feature table upon which to perform beta diversity rarefaction 147 Feature table upon which to perform beta diversity rarefaction
139 analyses. 148 analyses.
140 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') 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')
141 The beta diversity metric to be computed. 150 The beta diversity metric to be computed.
142 clustering_method : Str % Choices('upgma', 'nj') 151 clustering_method : Str % Choices('upgma', 'nj')
143 Samples can be clustered with neighbor joining or UPGMA. An arbitrary 152 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
144 rarefaction trial will be used for the tree, and the remaining trials 153 rarefaction trial will be used for the tree, and the remaining trials
145 are used to calculate the support of the internal nodes of that tree. 154 are used to calculate the support of the internal nodes of that tree.
153 phylogeny : Phylogeny[Rooted], optional 162 phylogeny : Phylogeny[Rooted], optional
154 Phylogenetic tree containing tip identifiers that correspond to the 163 Phylogenetic tree containing tip identifiers that correspond to the
155 feature identifiers in the table. This tree can contain tip ids that 164 feature identifiers in the table. This tree can contain tip ids that
156 are not present in the table, but all feature ids in the table must be 165 are not present in the table, but all feature ids in the table must be
157 present in this tree. [required for phylogenetic metrics] 166 present in this tree. [required for phylogenetic metrics]
158 correlation_method : Str % Choices('pearson', 'spearman'), optional 167 correlation_method : Str % Choices('spearman', 'pearson'), optional
159 The Mantel correlation test to be applied when computing correlation 168 The Mantel correlation test to be applied when computing correlation
160 between beta diversity distance matrices. 169 between beta diversity distance matrices.
161 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 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
162 The matplotlib color scheme to generate the heatmap with. 171 The matplotlib color scheme to generate the heatmap with.
163 172
164 Returns 173 Returns
165 ------- 174 -------
166 visualization : Visualization 175 visualization : Visualization
167 ]]></help> 176 ]]></help>
168 <macros> 177 <macros>
169 <import>qiime_citation.xml</import> 178 <import>qiime_citation.xml</import>
170 </macros> 179 </macros>
171 <expand macro="qiime_citation"/> 180 <expand macro="qiime_citation"/>
172 </tool> 181 </tool>