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comparison qiime2/qiime_diversity_core-metrics-phylogenetic.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_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.7"> 2 <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic"
3 <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</description> 3 version="2020.8">
4 <requirements> 4 <description>Core diversity metrics (phylogenetic and non- phylogenetic)</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 core-metrics-phylogenetic 9 qiime diversity core-metrics-phylogenetic
9 10
10 --i-table=$itable 11 --i-table=$itable
12
11 --i-phylogeny=$iphylogeny 13 --i-phylogeny=$iphylogeny
12 14
13 #if str($psamplingdepth): 15 --p-sampling-depth=$psamplingdepth
14 --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
15 #end if 29 #end if
16 30
17 #set $pnjobs = '${GALAXY_SLOTS:-4}' 31 --o-rarefied-table=orarefiedtable
18 #if str($pnjobs): 32
19 --p-n-jobs="$pnjobs" 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
20 #end if 67 #end if
21 68
22 69 ;
23 #if $input_files_mmetadatafile: 70 cp obraycurtispcoaresults.qza $obraycurtispcoaresults
24 #def list_dict_to_string(list_dict): 71
25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 72 ;
26 #for d in list_dict[1:]: 73 qiime tools export ounweightedunifracemperor.qzv --output-path out
27 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') 74 && mkdir -p '$ounweightedunifracemperor.files_path'
28 #end for
29 #return $file_list
30 #end def
31 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
32 #end if
33
34
35
36 --o-rarefied-table=orarefiedtable
37 --o-faith-pd-vector=ofaithpdvector
38 --o-observed-otus-vector=oobservedotusvector
39 --o-shannon-vector=oshannonvector
40 --o-evenness-vector=oevennessvector
41 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
42 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
43 --o-jaccard-distance-matrix=ojaccarddistancematrix
44 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
45 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
46 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
47 --o-jaccard-pcoa-results=ojaccardpcoaresults
48 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
49 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
50 --o-weighted-unifrac-emperor=oweightedunifracemperor
51 --o-jaccard-emperor=ojaccardemperor
52 --o-bray-curtis-emperor=obraycurtisemperor
53 ;
54 cp orarefiedtable.qza $orarefiedtable;
55 cp ofaithpdvector.qza $ofaithpdvector;
56 cp oobservedotusvector.qza $oobservedotusvector;
57 cp oshannonvector.qza $oshannonvector;
58 cp oevennessvector.qza $oevennessvector;
59 cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
60 cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
61 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
62 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
63 cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
64 cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
65 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
66 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
67 qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out && mkdir -p '$ounweightedunifracemperor.files_path'
68 && cp -r out/* '$ounweightedunifracemperor.files_path' 75 && cp -r out/* '$ounweightedunifracemperor.files_path'
69 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'; 76 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'
70 qiime tools export --input-path oweightedunifracemperor.qzv --output-path out && mkdir -p '$oweightedunifracemperor.files_path' 77
78 ;
79 qiime tools export oweightedunifracemperor.qzv --output-path out
80 && mkdir -p '$oweightedunifracemperor.files_path'
71 && cp -r out/* '$oweightedunifracemperor.files_path' 81 && cp -r out/* '$oweightedunifracemperor.files_path'
72 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'; 82 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'
73 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path' 83
84 ;
85 qiime tools export ojaccardemperor.qzv --output-path out
86 && mkdir -p '$ojaccardemperor.files_path'
74 && cp -r out/* '$ojaccardemperor.files_path' 87 && cp -r out/* '$ojaccardemperor.files_path'
75 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'; 88 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
76 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path' 89
90 ;
91 qiime tools export obraycurtisemperor.qzv --output-path out
92 && mkdir -p '$obraycurtisemperor.files_path'
77 && cp -r out/* '$obraycurtisemperor.files_path' 93 && cp -r out/* '$obraycurtisemperor.files_path'
78 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'; 94 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
79 ]]></command> 95
80 <inputs> 96 ]]></command>
81 <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"/> 97 <inputs>
82 <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"/> 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" />
83 <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" min="1" value="" type="integer"/> 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" />
84 100 <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" />
85 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> 101 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
86 <param label="--m-metadata-file: (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" type="data" format="tabular,qza,no_unzip.zip" /> 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" />
87 </repeat> 103 </repeat>
88 104 <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" optional="True" type="select">
89 </inputs> 105 <option selected="True" value="None">Selection is Optional</option>
90 <outputs> 106 <option value="Int % Range(1">Int % Range(1</option>
91 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/> 107 <option value="None">None</option>
92 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector"/> 108 </param>
93 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/> 109 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
94 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/> 110
95 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/> 111 </inputs>
96 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/> 112
97 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/> 113 <outputs>
98 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/> 114 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
99 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/> 115 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector" />
100 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/> 116 <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
101 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/> 117 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
102 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/> 118 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
103 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/> 119 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix" />
104 <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/> 120 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix" />
105 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/> 121 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
106 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/> 122 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
107 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/> 123 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults" />
108 </outputs> 124 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults" />
109 <help><![CDATA[ 125 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
110 Core diversity metrics (phylogenetic and non-phylogenetic) 126 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
111 ########################################################## 127 <data format="html" label="${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 ###############################################################
112 137
113 Applies a collection of diversity metrics (both phylogenetic and non- 138 Applies a collection of diversity metrics (both phylogenetic and non-
114 phylogenetic) to a feature table. 139 phylogenetic) to a feature table.
115 140
116 Parameters 141 Parameters
126 sampling_depth : Int % Range(1, None) 151 sampling_depth : Int % Range(1, None)
127 The total frequency that each sample should be rarefied to prior to 152 The total frequency that each sample should be rarefied to prior to
128 computing diversity metrics. 153 computing diversity metrics.
129 metadata : Metadata 154 metadata : Metadata
130 The sample metadata to use in the emperor plots. 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.
131 163
132 Returns 164 Returns
133 ------- 165 -------
134 rarefied_table : FeatureTable[Frequency] 166 rarefied_table : FeatureTable[Frequency]
135 The resulting rarefied feature table. 167 The resulting rarefied feature table.
136 faith_pd_vector : SampleData[AlphaDiversity] 168 faith_pd_vector : SampleData[AlphaDiversity]
137 Vector of Faith PD values by sample. 169 Vector of Faith PD values by sample.
138 observed_otus_vector : SampleData[AlphaDiversity] 170 observed_features_vector : SampleData[AlphaDiversity]
139 Vector of Observed OTUs values by sample. 171 Vector of Observed Features values by sample.
140 shannon_vector : SampleData[AlphaDiversity] 172 shannon_vector : SampleData[AlphaDiversity]
141 Vector of Shannon diversity values by sample. 173 Vector of Shannon diversity values by sample.
142 evenness_vector : SampleData[AlphaDiversity] 174 evenness_vector : SampleData[AlphaDiversity]
143 Vector of Pielou's evenness values by sample. 175 Vector of Pielou's evenness values by sample.
144 unweighted_unifrac_distance_matrix : DistanceMatrix 176 unweighted_unifrac_distance_matrix : DistanceMatrix
163 Emperor plot of the PCoA matrix computed from weighted UniFrac. 195 Emperor plot of the PCoA matrix computed from weighted UniFrac.
164 jaccard_emperor : Visualization 196 jaccard_emperor : Visualization
165 Emperor plot of the PCoA matrix computed from Jaccard. 197 Emperor plot of the PCoA matrix computed from Jaccard.
166 bray_curtis_emperor : Visualization 198 bray_curtis_emperor : Visualization
167 Emperor plot of the PCoA matrix computed from Bray-Curtis. 199 Emperor plot of the PCoA matrix computed from Bray-Curtis.
168 ]]></help> 200 ]]></help>
169 <macros> 201 <macros>
170 <import>qiime_citation.xml</import> 202 <import>qiime_citation.xml</import>
171 </macros> 203 </macros>
172 <expand macro="qiime_citation"/> 204 <expand macro="qiime_citation"/>
173 </tool> 205 </tool>