|
29
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Core diversity metrics (non-phylogenetic)</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime diversity core-metrics
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
|
12
|
|
|
13 --p-sampling-depth=$psamplingdepth
|
|
|
14 # if $input_files_mmetadatafile:
|
|
|
15 # def list_dict_to_string(list_dict):
|
|
|
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
17 # for d in list_dict[1:]:
|
|
|
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
19 # end for
|
|
|
20 # return $file_list
|
|
|
21 # end def
|
|
|
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
23 # end if
|
|
|
24
|
|
|
25 #if $pwithreplacement:
|
|
|
26 --p-with-replacement
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if str($pnjobs) != 'None':
|
|
|
30 --p-n-jobs=$pnjobs
|
|
|
31 #end if
|
|
|
32
|
|
|
33 --o-rarefied-table=orarefiedtable
|
|
|
34
|
|
|
35 --o-observed-features-vector=oobservedfeaturesvector
|
|
|
36
|
|
|
37 --o-shannon-vector=oshannonvector
|
|
|
38
|
|
|
39 --o-evenness-vector=oevennessvector
|
|
|
40
|
|
|
41 --o-jaccard-distance-matrix=ojaccarddistancematrix
|
|
|
42
|
|
|
43 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
|
|
|
44
|
|
|
45 --o-jaccard-pcoa-results=ojaccardpcoaresults
|
|
|
46
|
|
|
47 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
|
|
|
48
|
|
|
49 --o-jaccard-emperor=ojaccardemperor
|
|
|
50
|
|
|
51 --o-bray-curtis-emperor=obraycurtisemperor
|
|
|
52
|
|
|
53 #if str($examples) != 'None':
|
|
|
54 --examples=$examples
|
|
|
55 #end if
|
|
|
56
|
|
|
57 ;
|
|
|
58 cp obraycurtispcoaresults.qza $obraycurtispcoaresults
|
|
|
59
|
|
|
60 ;
|
|
|
61 qiime tools export ojaccardemperor.qzv --output-path out
|
|
|
62 && mkdir -p '$ojaccardemperor.files_path'
|
|
|
63 && cp -r out/* '$ojaccardemperor.files_path'
|
|
|
64 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
|
|
|
65
|
|
|
66 ;
|
|
|
67 qiime tools export obraycurtisemperor.qzv --output-path out
|
|
|
68 && mkdir -p '$obraycurtisemperor.files_path'
|
|
|
69 && cp -r out/* '$obraycurtisemperor.files_path'
|
|
|
70 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
|
|
|
71
|
|
|
72 ]]></command>
|
|
|
73 <inputs>
|
|
|
74 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data" />
|
|
|
75 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" />
|
|
|
76 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
77 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata to use in the emperor plots. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
|
|
|
78 </repeat>
|
|
|
79 <param label="--p-with-replacement: --p-with-replacement: / --p-no-with-replacement Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]" name="pwithreplacement" selected="False" type="boolean" />
|
|
|
80 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
|
|
|
81 <option selected="True" value="None">Selection is Optional</option>
|
|
|
82 <option value="Int % Range(1">Int % Range(1</option>
|
|
|
83 <option value="None">None</option>
|
|
|
84 </param>
|
|
|
85 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
86
|
|
|
87 </inputs>
|
|
|
88
|
|
|
89 <outputs>
|
|
|
90 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
|
|
|
91 <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
|
|
|
92 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
|
|
|
93 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
|
|
|
94 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
|
|
|
95 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
|
|
|
96 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
|
|
|
97 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
|
|
|
98 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
|
|
|
99 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
|
|
|
100
|
|
|
101 </outputs>
|
|
|
102
|
|
|
103 <help><![CDATA[
|
|
|
104 Core diversity metrics (non-phylogenetic)
|
|
|
105 ###############################################################
|
|
|
106
|
|
|
107 Applies a collection of diversity metrics (non-phylogenetic) to a feature
|
|
|
108 table.
|
|
|
109
|
|
|
110 Parameters
|
|
|
111 ----------
|
|
|
112 table : FeatureTable[Frequency]
|
|
|
113 The feature table containing the samples over which diversity metrics
|
|
|
114 should be computed.
|
|
|
115 sampling_depth : Int % Range(1, None)
|
|
|
116 The total frequency that each sample should be rarefied to prior to
|
|
|
117 computing diversity metrics.
|
|
|
118 metadata : Metadata
|
|
|
119 The sample metadata to use in the emperor plots.
|
|
|
120 with_replacement : Bool, optional
|
|
|
121 Rarefy with replacement by sampling from the multinomial distribution
|
|
|
122 instead of rarefying without replacement.
|
|
|
123 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
|
|
|
124 [beta methods only] - The number of concurrent jobs to use in
|
|
|
125 performing this calculation. May not exceed the number of available
|
|
|
126 physical cores. If n_jobs = 'auto', one job will be launched for each
|
|
|
127 identified CPU core on the host.
|
|
|
128
|
|
|
129 Returns
|
|
|
130 -------
|
|
|
131 rarefied_table : FeatureTable[Frequency]
|
|
|
132 The resulting rarefied feature table.
|
|
|
133 observed_features_vector : SampleData[AlphaDiversity]
|
|
|
134 Vector of Observed Features values by sample.
|
|
|
135 shannon_vector : SampleData[AlphaDiversity]
|
|
|
136 Vector of Shannon diversity values by sample.
|
|
|
137 evenness_vector : SampleData[AlphaDiversity]
|
|
|
138 Vector of Pielou's evenness values by sample.
|
|
|
139 jaccard_distance_matrix : DistanceMatrix
|
|
|
140 Matrix of Jaccard distances between pairs of samples.
|
|
|
141 bray_curtis_distance_matrix : DistanceMatrix
|
|
|
142 Matrix of Bray-Curtis distances between pairs of samples.
|
|
|
143 jaccard_pcoa_results : PCoAResults
|
|
|
144 PCoA matrix computed from Jaccard distances between samples.
|
|
|
145 bray_curtis_pcoa_results : PCoAResults
|
|
|
146 PCoA matrix computed from Bray-Curtis distances between samples.
|
|
|
147 jaccard_emperor : Visualization
|
|
|
148 Emperor plot of the PCoA matrix computed from Jaccard.
|
|
|
149 bray_curtis_emperor : Visualization
|
|
|
150 Emperor plot of the PCoA matrix computed from Bray-Curtis.
|
|
|
151 ]]></help>
|
|
|
152 <macros>
|
|
|
153 <import>qiime_citation.xml</import>
|
|
|
154 </macros>
|
|
|
155 <expand macro="qiime_citation"/>
|
|
|
156 </tool> |
