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comparison qiime2-2020.8/qiime_diversity_core-metrics-phylogenetic.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-phylogenetic" name="qiime diversity core-metrics-phylogenetic"
3 version="2020.8">
4 <description>Core diversity metrics (phylogenetic and non- phylogenetic)</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity core-metrics-phylogenetic
10
11 --i-table=$itable
12
13 --i-phylogeny=$iphylogeny
14
15 --p-sampling-depth=$psamplingdepth
16 # if $input_files_mmetadatafile:
17 # def list_dict_to_string(list_dict):
18 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
19 # for d in list_dict[1:]:
20 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
21 # end for
22 # return $file_list
23 # end def
24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
25 # end if
26
27 #if str($pnjobsorthreads) != 'None':
28 --p-n-jobs-or-threads=$pnjobsorthreads
29 #end if
30
31 --o-rarefied-table=orarefiedtable
32
33 --o-faith-pd-vector=ofaithpdvector
34
35 --o-observed-features-vector=oobservedfeaturesvector
36
37 --o-shannon-vector=oshannonvector
38
39 --o-evenness-vector=oevennessvector
40
41 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
42
43 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
44
45 --o-jaccard-distance-matrix=ojaccarddistancematrix
46
47 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
48
49 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
50
51 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
52
53 --o-jaccard-pcoa-results=ojaccardpcoaresults
54
55 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
56
57 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
58
59 --o-weighted-unifrac-emperor=oweightedunifracemperor
60
61 --o-jaccard-emperor=ojaccardemperor
62
63 --o-bray-curtis-emperor=obraycurtisemperor
64
65 #if str($examples) != 'None':
66 --examples=$examples
67 #end if
68
69 ;
70 cp obraycurtispcoaresults.qza $obraycurtispcoaresults
71
72 ;
73 qiime tools export ounweightedunifracemperor.qzv --output-path out
74 && mkdir -p '$ounweightedunifracemperor.files_path'
75 && cp -r out/* '$ounweightedunifracemperor.files_path'
76 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'
77
78 ;
79 qiime tools export oweightedunifracemperor.qzv --output-path out
80 && mkdir -p '$oweightedunifracemperor.files_path'
81 && cp -r out/* '$oweightedunifracemperor.files_path'
82 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'
83
84 ;
85 qiime tools export ojaccardemperor.qzv --output-path out
86 && mkdir -p '$ojaccardemperor.files_path'
87 && cp -r out/* '$ojaccardemperor.files_path'
88 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
89
90 ;
91 qiime tools export obraycurtisemperor.qzv --output-path out
92 && mkdir -p '$obraycurtisemperor.files_path'
93 && cp -r out/* '$obraycurtisemperor.files_path'
94 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
95
96 ]]></command>
97 <inputs>
98 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data" />
99 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
100 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" />
101 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
102 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata to use in the emperor plots. will be merged) [required]" name="additional_input" optional="False" type="data" />
103 </repeat>
104 <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" optional="True" type="select">
105 <option selected="True" value="None">Selection is Optional</option>
106 <option value="Int % Range(1">Int % Range(1</option>
107 <option value="None">None</option>
108 </param>
109 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
110
111 </inputs>
112
113 <outputs>
114 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
115 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector" />
116 <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
117 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
118 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
119 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix" />
120 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix" />
121 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
122 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
123 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults" />
124 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults" />
125 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
126 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
127 <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.html" name="ounweightedunifracemperor" />
128 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.html" name="oweightedunifracemperor" />
129 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
130 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
131
132 </outputs>
133
134 <help><![CDATA[
135 Core diversity metrics (phylogenetic and non- phylogenetic)
136 ###############################################################
137
138 Applies a collection of diversity metrics (both phylogenetic and non-
139 phylogenetic) to a feature table.
140
141 Parameters
142 ----------
143 table : FeatureTable[Frequency]
144 The feature table containing the samples over which diversity metrics
145 should be computed.
146 phylogeny : Phylogeny[Rooted]
147 Phylogenetic tree containing tip identifiers that correspond to the
148 feature identifiers in the table. This tree can contain tip ids that
149 are not present in the table, but all feature ids in the table must be
150 present in this tree.
151 sampling_depth : Int % Range(1, None)
152 The total frequency that each sample should be rarefied to prior to
153 computing diversity metrics.
154 metadata : Metadata
155 The sample metadata to use in the emperor plots.
156 n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional
157 [beta/beta-phylogenetic methods only] - The number of concurrent jobs
158 or CPU threads to use in performing this calculation. Individual
159 methods will create jobs/threads as implemented in q2-diversity-lib
160 dependencies. May not exceed the number of available physical cores. If
161 n_jobs_or_threads = 'auto', one thread/job will be created for each
162 identified CPU core on the host.
163
164 Returns
165 -------
166 rarefied_table : FeatureTable[Frequency]
167 The resulting rarefied feature table.
168 faith_pd_vector : SampleData[AlphaDiversity]
169 Vector of Faith PD values by sample.
170 observed_features_vector : SampleData[AlphaDiversity]
171 Vector of Observed Features values by sample.
172 shannon_vector : SampleData[AlphaDiversity]
173 Vector of Shannon diversity values by sample.
174 evenness_vector : SampleData[AlphaDiversity]
175 Vector of Pielou's evenness values by sample.
176 unweighted_unifrac_distance_matrix : DistanceMatrix
177 Matrix of unweighted UniFrac distances between pairs of samples.
178 weighted_unifrac_distance_matrix : DistanceMatrix
179 Matrix of weighted UniFrac distances between pairs of samples.
180 jaccard_distance_matrix : DistanceMatrix
181 Matrix of Jaccard distances between pairs of samples.
182 bray_curtis_distance_matrix : DistanceMatrix
183 Matrix of Bray-Curtis distances between pairs of samples.
184 unweighted_unifrac_pcoa_results : PCoAResults
185 PCoA matrix computed from unweighted UniFrac distances between samples.
186 weighted_unifrac_pcoa_results : PCoAResults
187 PCoA matrix computed from weighted UniFrac distances between samples.
188 jaccard_pcoa_results : PCoAResults
189 PCoA matrix computed from Jaccard distances between samples.
190 bray_curtis_pcoa_results : PCoAResults
191 PCoA matrix computed from Bray-Curtis distances between samples.
192 unweighted_unifrac_emperor : Visualization
193 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
194 weighted_unifrac_emperor : Visualization
195 Emperor plot of the PCoA matrix computed from weighted UniFrac.
196 jaccard_emperor : Visualization
197 Emperor plot of the PCoA matrix computed from Jaccard.
198 bray_curtis_emperor : Visualization
199 Emperor plot of the PCoA matrix computed from Bray-Curtis.
200 ]]></help>
201 <macros>
202 <import>qiime_citation.xml</import>
203 </macros>
204 <expand macro="qiime_citation"/>
205 </tool>