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comparison qiime2/qiime_diversity_core-metrics-phylogenetic.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.4">
3 <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity core-metrics-phylogenetic
9
10 --i-table=$itable
11 --i-phylogeny=$iphylogeny
12 --p-sampling-depth="$psamplingdepth"
13
14 #set $pnjobs = '${GALAXY_SLOTS:-4}'
15 #if str($pnjobs):
16 --p-n-jobs="$pnjobs"
17 #end if
18
19 #def list_dict_to_string(list_dict):
20 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
21 #for d in list_dict[1:]:
22 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
23 #end for
24 #return $file_list
25 #end def
26
27 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
28
29
30 --o-rarefied-table=orarefiedtable
31 --o-faith-pd-vector=ofaithpdvector
32 --o-observed-otus-vector=oobservedotusvector
33 --o-shannon-vector=oshannonvector
34 --o-evenness-vector=oevennessvector
35 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
36 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
37 --o-jaccard-distance-matrix=ojaccarddistancematrix
38 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
39 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
40 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
41 --o-jaccard-pcoa-results=ojaccardpcoaresults
42 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
43 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
44 --o-weighted-unifrac-emperor=oweightedunifracemperor
45 --o-jaccard-emperor=ojaccardemperor
46 --o-bray-curtis-emperor=obraycurtisemperor
47 ;
48 cp orarefiedtable.qza $orarefiedtable;
49 cp ofaithpdvector.qza $ofaithpdvector;
50 cp oobservedotusvector.qza $oobservedotusvector;
51 cp oshannonvector.qza $oshannonvector;
52 cp oevennessvector.qza $oevennessvector;
53 cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
54 cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
55 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
56 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
57 cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
58 cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
59 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
60 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
61 qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out && mkdir -p '$ounweightedunifracemperor.files_path'
62 && cp -r out/* '$ounweightedunifracemperor.files_path'
63 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
64 qiime tools export --input-path oweightedunifracemperor.qzv --output-path out && mkdir -p '$oweightedunifracemperor.files_path'
65 && cp -r out/* '$oweightedunifracemperor.files_path'
66 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
67 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path'
68 && cp -r out/* '$ojaccardemperor.files_path'
69 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
70 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path'
71 && cp -r out/* '$obraycurtisemperor.files_path'
72 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
73 ]]></command>
74 <inputs>
75 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
76 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/>
77 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
78
79 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
80 <param label="--m-metadata-file: (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
81 </repeat>
82
83 </inputs>
84 <outputs>
85 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
86 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector"/>
87 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
88 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
89 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
90 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/>
91 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/>
92 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
93 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
94 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/>
95 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/>
96 <data format="qza" label="${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 ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/>
99 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/>
100 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
101 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
102 </outputs>
103 <help><![CDATA[
104 Core diversity metrics (phylogenetic and non-phylogenetic)
105 ##########################################################
106
107 Applies a collection of diversity metrics (both phylogenetic and non-
108 phylogenetic) to a feature 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 phylogeny : Phylogeny[Rooted]
116 Phylogenetic tree containing tip identifiers that correspond to the
117 feature identifiers in the table. This tree can contain tip ids that
118 are not present in the table, but all feature ids in the table must be
119 present in this tree.
120 sampling_depth : Int % Range(1, None)
121 The total frequency that each sample should be rarefied to prior to
122 computing diversity metrics.
123 metadata : Metadata
124 The sample metadata to use in the emperor plots.
125
126 Returns
127 -------
128 rarefied_table : FeatureTable[Frequency]
129 The resulting rarefied feature table.
130 faith_pd_vector : SampleData[AlphaDiversity]
131 Vector of Faith PD values by sample.
132 observed_otus_vector : SampleData[AlphaDiversity]
133 Vector of Observed OTUs values by sample.
134 shannon_vector : SampleData[AlphaDiversity]
135 Vector of Shannon diversity values by sample.
136 evenness_vector : SampleData[AlphaDiversity]
137 Vector of Pielou's evenness values by sample.
138 unweighted_unifrac_distance_matrix : DistanceMatrix
139 Matrix of unweighted UniFrac distances between pairs of samples.
140 weighted_unifrac_distance_matrix : DistanceMatrix
141 Matrix of weighted UniFrac distances between pairs of samples.
142 jaccard_distance_matrix : DistanceMatrix
143 Matrix of Jaccard distances between pairs of samples.
144 bray_curtis_distance_matrix : DistanceMatrix
145 Matrix of Bray-Curtis distances between pairs of samples.
146 unweighted_unifrac_pcoa_results : PCoAResults
147 PCoA matrix computed from unweighted UniFrac distances between samples.
148 weighted_unifrac_pcoa_results : PCoAResults
149 PCoA matrix computed from weighted UniFrac distances between samples.
150 jaccard_pcoa_results : PCoAResults
151 PCoA matrix computed from Jaccard distances between samples.
152 bray_curtis_pcoa_results : PCoAResults
153 PCoA matrix computed from Bray-Curtis distances between samples.
154 unweighted_unifrac_emperor : Visualization
155 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
156 weighted_unifrac_emperor : Visualization
157 Emperor plot of the PCoA matrix computed from weighted UniFrac.
158 jaccard_emperor : Visualization
159 Emperor plot of the PCoA matrix computed from Jaccard.
160 bray_curtis_emperor : Visualization
161 Emperor plot of the PCoA matrix computed from Bray-Curtis.
162 ]]></help>
163 <macros>
164 <import>qiime_citation.xml</import>
165 </macros>
166 <expand macro="qiime_citation"/>
167 </tool>