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comparison qiime2/qiime_emperor_biplot.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_emperor_biplot" name="qiime emperor biplot" version="2019.4">
3 <description> - Visualize and Interact with Principal Coordinates Analysis Biplot</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime emperor biplot
9
10 --i-biplot=$ibiplot
11
12
13 #def list_dict_to_string(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
17 #end for
18 #return $file_list
19 #end def
20
21 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
22 --m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile)
23
24
25 #if $pignoremissingsamples:
26 --p-ignore-missing-samples
27 #end if
28
29 #if $pnumberoffeatures:
30 --p-number-of-features=$pnumberoffeatures
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 <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/>
41 <param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
42 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>
43
44 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
45 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
46 </repeat>
47
48 <repeat name="m_feature_metadatafile" optional="True" title="--m-metadata-file">
49 <param label="--m-feature-metadata-file: (multiple arguments will be merged) The feature metadata (useful to manipulate the arrows in the plot). [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
50 </repeat>
51
52 </inputs>
53 <outputs>
54 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
55 </outputs>
56 <help><![CDATA[
57 Visualize and Interact with Principal Coordinates Analysis Biplot
58 #################################################################
59
60 Generates an interactive ordination biplot where the user can visually
61 integrate sample and feature metadata.
62
63 Parameters
64 ----------
65 biplot : PCoAResults % Properties('biplot')
66 The principal coordinates matrix to be plotted.
67 sample_metadata : Metadata
68 The sample metadata
69 feature_metadata : Metadata, optional
70 The feature metadata (useful to manipulate the arrows in the plot).
71 ignore_missing_samples : Bool, optional
72 This will suppress the error raised when the coordinates matrix
73 contains samples that are not present in the metadata. Samples without
74 metadata are included by setting all metadata values to: "This sample
75 has no metadata". This flag is only applied if at least one sample is
76 present in both the coordinates matrix and the metadata.
77 number_of_features : Int % Range(1, None), optional
78 The number of most important features (arrows) to display in the
79 ordination.
80
81 Returns
82 -------
83 visualization : Visualization
84 ]]></help>
85 <macros>
86 <import>qiime_citation.xml</import>
87 </macros>
88 <expand macro="qiime_citation"/>
89 </tool>