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comparison qiime2-2020.8/qiime_emperor_plot.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_plot" name="qiime emperor plot"
3 version="2020.8">
4 <description>Visualize and Interact with Principal Coordinates Analysis Plots</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime emperor plot
10
11 --i-pcoa=$ipcoa
12 # if $input_files_mmetadatafile:
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-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
22
23 #if str($pcustomaxes):
24 --p-custom-axes=$pcustomaxes
25 #end if
26 #if $pignoremissingsamples:
27 --p-ignore-missing-samples
28 #end if
29
30 --o-visualization=ovisualization
31
32 #if str($examples) != 'None':
33 --examples=$examples
34 #end if
35
36 ;
37 cp odistancematrix.qza $odistancematrix
38
39 ;
40 qiime tools export ovisualization.qzv --output-path out
41 && mkdir -p '$ovisualization.files_path'
42 && cp -r out/* '$ovisualization.files_path'
43 && mv '$ovisualization.files_path/index.html' '$ovisualization'
44
45 ;
46 qiime tools export ovisualization.qzv --output-path out
47 && mkdir -p '$ovisualization.files_path'
48 && cp -r out/* '$ovisualization.files_path'
49 && mv '$ovisualization.files_path/index.html' '$ovisualization'
50
51 ]]></command>
52 <inputs>
53 <param format="qza,no_unzip.zip" label="--i-pcoa: ARTIFACT The principal coordinates matrix to be plotted. PCoAResults [required]" name="ipcoa" optional="False" type="data" />
54 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
55 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
56 </repeat>
57 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="False" type="text" />
58 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
65
66 </outputs>
67
68 <help><![CDATA[
69 Visualize and Interact with Principal Coordinates Analysis Plots
70 ###############################################################
71
72 Generates an interactive ordination plot where the user can visually
73 integrate sample metadata.
74
75 Parameters
76 ----------
77 pcoa : PCoAResults
78 The principal coordinates matrix to be plotted.
79 metadata : Metadata
80 The sample metadata.
81 custom_axes : List[Str], optional
82 Numeric sample metadata columns that should be included as axes in the
83 Emperor plot.
84 ignore_missing_samples : Bool, optional
85 This will suppress the error raised when the coordinates matrix
86 contains samples that are not present in the metadata. Samples without
87 metadata are included by setting all metadata values to: "This sample
88 has no metadata". This flag is only applied if at least one sample is
89 present in both the coordinates matrix and the metadata.
90
91 Returns
92 -------
93 visualization : Visualization
94 ]]></help>
95 <macros>
96 <import>qiime_citation.xml</import>
97 </macros>
98 <expand macro="qiime_citation"/>
99 </tool>