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comparison qiime2/qiime_diversity_core-metrics.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" name="qiime diversity core-metrics" version="2019.4">
3 <description> - Core diversity metrics (non-phylogenetic)</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity core-metrics
9
10 --i-table=$itable
11 --p-sampling-depth="$psamplingdepth"
12
13 #set $pnjobs = '${GALAXY_SLOTS:-4}'
14 #if str($pnjobs):
15 --p-n-jobs="$pnjobs"
16 #end if
17
18 #def list_dict_to_string(list_dict):
19 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
20 #for d in list_dict[1:]:
21 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
22 #end for
23 #return $file_list
24 #end def
25
26 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
27
28
29 --o-rarefied-table=orarefiedtable
30 --o-observed-otus-vector=oobservedotusvector
31 --o-shannon-vector=oshannonvector
32 --o-evenness-vector=oevennessvector
33 --o-jaccard-distance-matrix=ojaccarddistancematrix
34 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
35 --o-jaccard-pcoa-results=ojaccardpcoaresults
36 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
37 --o-jaccard-emperor=ojaccardemperor
38 --o-bray-curtis-emperor=obraycurtisemperor
39 ;
40 cp orarefiedtable.qza $orarefiedtable;
41 cp oobservedotusvector.qza $oobservedotusvector;
42 cp oshannonvector.qza $oshannonvector;
43 cp oevennessvector.qza $oevennessvector;
44 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
45 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
46 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
47 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
48 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path'
49 && cp -r out/* '$ojaccardemperor.files_path'
50 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
51 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path'
52 && cp -r out/* '$obraycurtisemperor.files_path'
53 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
54 ]]></command>
55 <inputs>
56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
57 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
58
59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
60 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
61 </repeat>
62
63 </inputs>
64 <outputs>
65 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
66 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
67 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
68 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
69 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
70 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
71 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
72 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
73 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
74 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
75 </outputs>
76 <help><![CDATA[
77 Core diversity metrics (non-phylogenetic)
78 #########################################
79
80 Applies a collection of diversity metrics (non-phylogenetic) to a feature
81 table.
82
83 Parameters
84 ----------
85 table : FeatureTable[Frequency]
86 The feature table containing the samples over which diversity metrics
87 should be computed.
88 sampling_depth : Int % Range(1, None)
89 The total frequency that each sample should be rarefied to prior to
90 computing diversity metrics.
91 metadata : Metadata
92 The sample metadata to use in the emperor plots.
93
94 Returns
95 -------
96 rarefied_table : FeatureTable[Frequency]
97 The resulting rarefied feature table.
98 observed_otus_vector : SampleData[AlphaDiversity]
99 Vector of Observed OTUs values by sample.
100 shannon_vector : SampleData[AlphaDiversity]
101 Vector of Shannon diversity values by sample.
102 evenness_vector : SampleData[AlphaDiversity]
103 Vector of Pielou's evenness values by sample.
104 jaccard_distance_matrix : DistanceMatrix
105 Matrix of Jaccard distances between pairs of samples.
106 bray_curtis_distance_matrix : DistanceMatrix
107 Matrix of Bray-Curtis distances between pairs of samples.
108 jaccard_pcoa_results : PCoAResults
109 PCoA matrix computed from Jaccard distances between samples.
110 bray_curtis_pcoa_results : PCoAResults
111 PCoA matrix computed from Bray-Curtis distances between samples.
112 jaccard_emperor : Visualization
113 Emperor plot of the PCoA matrix computed from Jaccard.
114 bray_curtis_emperor : Visualization
115 Emperor plot of the PCoA matrix computed from Bray-Curtis.
116 ]]></help>
117 <macros>
118 <import>qiime_citation.xml</import>
119 </macros>
120 <expand macro="qiime_citation"/>
121 </tool>