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comparison qiime2-2020.8/qiime_taxa_barplot.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot"
3 version="2020.8">
4 <description>Visualize taxonomy with an interactive bar plot</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime taxa barplot
10
11 --i-table=$itable
12
13 --i-taxonomy=$itaxonomy
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 --o-visualization=ovisualization
26
27 #if str($examples) != 'None':
28 --examples=$examples
29 #end if
30
31 ;
32 cp otesttable.qza $otesttable
33
34 ;
35 qiime tools export ovisualization.qzv --output-path out
36 && mkdir -p '$ovisualization.files_path'
37 && cp -r out/* '$ovisualization.files_path'
38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
39
40 ;
41 qiime tools export ovisualization.qzv --output-path out
42 && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
45
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data" />
49 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
51 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
52 </repeat>
53 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
54
55 </inputs>
56
57 <outputs>
58 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
59
60 </outputs>
61
62 <help><![CDATA[
63 Visualize taxonomy with an interactive bar plot
64 ###############################################################
65
66 This visualizer produces an interactive barplot visualization of
67 taxonomies. Interactive features include multi-level sorting, plot
68 recoloring, sample relabeling, and SVG figure export.
69
70 Parameters
71 ----------
72 table : FeatureTable[Frequency]
73 Feature table to visualize at various taxonomic levels.
74 taxonomy : FeatureData[Taxonomy]
75 Taxonomic annotations for features in the provided feature table. All
76 features in the feature table must have a corresponding taxonomic
77 annotation. Taxonomic annotations that are not present in the feature
78 table will be ignored.
79 metadata : Metadata
80 The sample metadata.
81
82 Returns
83 -------
84 visualization : Visualization
85 ]]></help>
86 <macros>
87 <import>qiime_citation.xml</import>
88 </macros>
89 <expand macro="qiime_citation"/>
90 </tool>