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comparison qiime2/qiime_emperor_biplot.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_biplot" name="qiime emperor biplot"
3 version="2020.8">
4 <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime emperor biplot
10
11 --i-biplot=$ibiplot
12 # if $input_files_msamplemetadatafile:
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 + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
21 # end if
22 # if $input_files_mfeaturemetadatafile:
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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
27 # end for
28 # return $file_list
29 # end def
30 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
31 # end if
32
33 #if $pignoremissingsamples:
34 --p-ignore-missing-samples
35 #end if
36
37 #if $pinvert:
38 --p-invert
39 #end if
40
41 --p-number-of-features=$pnumberoffeatures
42
43 --o-visualization=ovisualization
44
45 #if str($examples) != 'None':
46 --examples=$examples
47 #end if
48
49 ;
50 cp odistancematrix.qza $odistancematrix
51
52 ;
53 qiime tools export ovisualization.qzv --output-path out
54 && mkdir -p '$ovisualization.files_path'
55 && cp -r out/* '$ovisualization.files_path'
56 && mv '$ovisualization.files_path/index.html' '$ovisualization'
57
58 ]]></command>
59 <inputs>
60 <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" />
61 <repeat name="input_files_msamplemetadatafile" optional="False" title="--m-sample-metadata-file">
62 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
63 </repeat>
64 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
65 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA... (multiple The feature metadata (useful to manipulate the arrows arguments will in the plot). be merged) [optional]" name="additional_input" optional="True" type="data" />
66 </repeat>
67 <param label="--p-ignore-missing-samples: --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" />
68 <param label="--p-invert: --p-invert: / --p-no-invert If specified, the point and arrow coordinates will be swapped. [default: False]" name="pinvert" selected="False" type="boolean" />
69 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin). [default: 5]" min="1" name="pnumberoffeatures" optional="True" type="integer" value="5" />
70 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
71
72 </inputs>
73
74 <outputs>
75 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
76
77 </outputs>
78
79 <help><![CDATA[
80 Visualize and Interact with Principal Coordinates Analysis Biplot
81 ###############################################################
82
83 Generates an interactive ordination biplot where the user can visually
84 integrate sample and feature metadata. Vectors representing the n most
85 important features are then plotted in the emperor visualization (5
86 largest, by default).
87
88 Parameters
89 ----------
90 biplot : PCoAResults % Properties('biplot')
91 The principal coordinates matrix to be plotted.
92 sample_metadata : Metadata
93 The sample metadata
94 feature_metadata : Metadata, optional
95 The feature metadata (useful to manipulate the arrows in the plot).
96 ignore_missing_samples : Bool, optional
97 This will suppress the error raised when the coordinates matrix
98 contains samples that are not present in the metadata. Samples without
99 metadata are included by setting all metadata values to: "This sample
100 has no metadata". This flag is only applied if at least one sample is
101 present in both the coordinates matrix and the metadata.
102 invert : Bool, optional
103 If specified, the point and arrow coordinates will be swapped.
104 number_of_features : Int % Range(1, None), optional
105 The number of most important features (arrows) to display in the
106 ordination. “Importance” is calculated for each feature based on the
107 vector’s magnitude (euclidean distance from origin).
108
109 Returns
110 -------
111 visualization : Visualization
112 ]]></help>
113 <macros>
114 <import>qiime_citation.xml</import>
115 </macros>
116 <expand macro="qiime_citation"/>
117 </tool>