0
|
1 <?xml version="1.0" ?>
|
|
2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4">
|
|
3 <description> - Visualize taxonomy with an interactive bar plot</description>
|
|
4 <requirements>
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
6 </requirements>
|
|
7 <command><![CDATA[
|
|
8 qiime taxa barplot
|
|
9
|
6
|
10
|
|
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
|
|
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
|
|
13 --i-taxonomy '$tax'
|
|
14 #else:
|
|
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
|
|
16 --i-taxonomy '$tax'
|
|
17 #end if
|
|
18
|
|
19
|
0
|
20 --i-table=$itable
|
|
21
|
|
22 #if $input_files_mmetadatafile:
|
|
23 #def list_dict_to_string(list_dict):
|
|
24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
25 #for d in list_dict[1:]:
|
|
26 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
27 #end for
|
|
28 #return $file_list
|
|
29 #end def
|
|
30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
31 #end if
|
|
32
|
|
33 --o-visualization=ovisualization
|
|
34 ;
|
|
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
36 && cp -r out/* '$ovisualization.files_path'
|
|
37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
38 ]]></command>
|
|
39 <inputs>
|
|
40
|
6
|
41 <conditional name="id_to_taxonomy_fp" optional="True">
|
|
42 <param name="selector" type="select" label="Reference taxonomy to query">
|
|
43 <option value="cached">Public databases</option>
|
|
44 <option value="history">Databases from your history</option>
|
|
45 </param>
|
|
46 <when value="cached">
|
|
47 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
|
|
48 <options from_data_table="qiime_taxonomy" />
|
|
49 </param>
|
|
50 </when>
|
|
51 <when value="history">
|
|
52 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
|
|
53 </when>
|
|
54 </conditional>
|
|
55
|
|
56
|
|
57 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/>
|
|
58
|
|
59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
|
|
60 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" optional="False" />
|
0
|
61 </repeat>
|
|
62
|
|
63 </inputs>
|
|
64 <outputs>
|
|
65 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
66 </outputs>
|
|
67 <help><![CDATA[
|
|
68 Visualize taxonomy with an interactive bar plot
|
|
69 ###############################################
|
|
70
|
|
71 This visualizer produces an interactive barplot visualization of
|
|
72 taxonomies. Interactive features include multi-level sorting, plot
|
|
73 recoloring, sample relabeling, and SVG figure export.
|
|
74
|
|
75 Parameters
|
|
76 ----------
|
|
77 table : FeatureTable[Frequency]
|
|
78 Feature table to visualize at various taxonomic levels.
|
|
79 taxonomy : FeatureData[Taxonomy]
|
|
80 Taxonomic annotations for features in the provided feature table. All
|
|
81 features in the feature table must have a corresponding taxonomic
|
|
82 annotation. Taxonomic annotations that are not present in the feature
|
|
83 table will be ignored.
|
|
84 metadata : Metadata
|
|
85 The sample metadata.
|
|
86
|
|
87 Returns
|
|
88 -------
|
|
89 visualization : Visualization
|
|
90 ]]></help>
|
|
91 <macros>
|
|
92 <import>qiime_citation.xml</import>
|
|
93 </macros>
|
|
94 <expand macro="qiime_citation"/>
|
|
95 </tool>
|