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comparison qiime2/qiime_taxa_barplot.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2018.4">
3 <description>- Visualize taxonomy with an interactive bar plot</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime taxa barplot
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 #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 + ' --m-metadata-file=' + 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($input_files_mmetadatafile)
28 --i-table=$itable --o-visualization=ovisualization
29
30 #if str($cmdconfig) != 'None':
31 --cmd-config=$cmdconfig
32 #end if
33 ;
34 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
35 && cp -r out/* '$ovisualization.files_path'
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37 ]]>
38 </command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/>
41
42 <conditional name="id_to_taxonomy_fp" optional="True">
43 <param name="selector" type="select" label="Reference taxonomy to query">
44 <option value="cached">Public databases</option>
45 <option value="history">Databases from your history</option>
46 </param>
47 <when value="cached">
48 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
49 <options from_data_table="qiime_taxonomy" />
50 </param>
51 </when>
52 <when value="history">
53 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
54 </when>
55 </conditional>
56
57 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
58 <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. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
59 </repeat>
60
61 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
62 </inputs>
63 <outputs>
64 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
65 </outputs>
66 <help>
67 <![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 \
91 ]]>
92 </help>
93 <macros>
94 <import>qiime_citation.xml</import>
95 </macros>
96 <expand macro="qiime_citation" />
97 </tool>