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comparison qiime_diversity_core-metrics.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2018.4">
3 <description> - Core diversity metrics (non-phylogenetic)</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity core-metrics --i-table=$itable
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-sampling-depth="$psamplingdepth"
19
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 --o-jaccard-pcoa-results=ojaccardpcoaresults --o-jaccard-emperor=ojaccardemperor --o-shannon-vector=oshannonvector --o-bray-curtis-distance-matrix=obraycurtisdistancematrix --o-bray-curtis-emperor=obraycurtisemperor --o-rarefied-table=orarefiedtable --o-jaccard-distance-matrix=ojaccarddistancematrix
25
26 #set $pnjobs = '${GALAXY_SLOTS:-4}'
27
28 #if str($pnjobs):
29 --p-n-jobs="$pnjobs"
30 #end if
31
32 --o-evenness-vector=oevennessvector --o-bray-curtis-pcoa-results=obraycurtispcoaresults --o-observed-otus-vector=oobservedotusvector;
33
34 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
35
36 qiime tools export ojaccardemperor.qzv --output-dir out && mkdir -p '$ojaccardemperor.files_path'
37 && cp -r out/* '$ojaccardemperor.files_path'
38 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
39
40 cp oshannonvector.qza $oshannonvector;
41 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
42
43 qiime tools export obraycurtisemperor.qzv --output-dir out && mkdir -p '$obraycurtisemperor.files_path'
44 && cp -r out/* '$obraycurtisemperor.files_path'
45 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
46
47 cp orarefiedtable.qza $orarefiedtable;
48 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
49 cp oevennessvector.qza $oevennessvector;
50 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
51 cp oobservedotusvector.qza $oobservedotusvector;
52 ]]></command>
53 <inputs>
54 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
55 <param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text"/>
56 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
57 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
58 </repeat>
59 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
60 </inputs>
61 <outputs>
62 <data format="qza" label="${tool.name} on ${on_string}: rarefied-table.qza" name="orarefiedtable"/>
63 <data format="qza" label="${tool.name} on ${on_string}: observed-otus-vector.qza" name="oobservedotusvector"/>
64 <data format="qza" label="${tool.name} on ${on_string}: shannon-vector.qza" name="oshannonvector"/>
65 <data format="qza" label="${tool.name} on ${on_string}: evenness-vector.qza" name="oevennessvector"/>
66 <data format="qza" label="${tool.name} on ${on_string}: jaccard-distance-matrix.qza" name="ojaccarddistancematrix"/>
67 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-distance-matrix.qza" name="obraycurtisdistancematrix"/>
68 <data format="qza" label="${tool.name} on ${on_string}: jaccard-pcoa-results.qza" name="ojaccardpcoaresults"/>
69 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-pcoa-results.qza" name="obraycurtispcoaresults"/>
70 <data format="html" label="${tool.name} on ${on_string}: jaccard-emperor.qzv" name="ojaccardemperor"/>
71 <data format="html" label="${tool.name} on ${on_string}: bray-curtis-emperor.qzv" name="obraycurtisemperor"/>
72 </outputs>
73 <help><![CDATA[
74 Core diversity metrics (non-phylogenetic)
75 -----------------------------------------
76
77 Applies a collection of diversity metrics (non-phylogenetic) to a feature
78 table.
79
80 Parameters
81 ----------
82 table : FeatureTable[Frequency]
83 The feature table containing the samples over which diversity metrics
84 should be computed.
85 sampling_depth : Int % Range(1, None)
86 The total frequency that each sample should be rarefied to prior to
87 computing diversity metrics.
88 metadata : Metadata
89 The sample metadata to use in the emperor plots.
90
91 Returns
92 -------
93 rarefied_table : FeatureTable[Frequency]
94 The resulting rarefied feature table.
95 observed_otus_vector : SampleData[AlphaDiversity]
96 Vector of Observed OTUs values by sample.
97 shannon_vector : SampleData[AlphaDiversity]
98 Vector of Shannon diversity values by sample.
99 evenness_vector : SampleData[AlphaDiversity]
100 Vector of Pielou's evenness values by sample.
101 jaccard_distance_matrix : DistanceMatrix
102 Matrix of Jaccard distances between pairs of samples.
103 bray_curtis_distance_matrix : DistanceMatrix
104 Matrix of Bray-Curtis distances between pairs of samples.
105 jaccard_pcoa_results : PCoAResults
106 PCoA matrix computed from Jaccard distances between samples.
107 bray_curtis_pcoa_results : PCoAResults
108 PCoA matrix computed from Bray-Curtis distances between samples.
109 jaccard_emperor : Visualization
110 Emperor plot of the PCoA matrix computed from Jaccard.
111 bray_curtis_emperor : Visualization
112 Emperor plot of the PCoA matrix computed from Bray-Curtis.
113 ]]>
114 </help>
115 </tool>