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comparison qiime2-2020.8/qiime_diversity_core-metrics.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_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>