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comparison qiime2/qiime_emperor_plot.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_plot" name="qiime emperor plot" version="2019.4">
3 <description> - Visualize and Interact with Principal Coordinates Analysis Plots</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime emperor plot
9
10 --i-pcoa=$ipcoa
11
12
13 #if $input_files_mmetadatafile:
14 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if
23
24
25 #if str($pcustomaxes):
26 --p-custom-axes="$pcustomaxes"
27 #end if
28
29 #if $pignoremissingsamples:
30 --p-ignore-missing-samples
31 #end if
32
33 --o-visualization=ovisualization
34 ;
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
36 && cp -r out/* '$ovisualization.files_path'
37 && mv '$ovisualization.files_path/index.html' '$ovisualization'
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-pcoa: ARTIFACT The principal coordinates matrix to be plotted. PCoAResults [required]" name="ipcoa" optional="False" type="data"/>
41 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>
42 <param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
43
44 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
45 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
46 </repeat>
47
48 </inputs>
49 <outputs>
50 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
51 </outputs>
52 <help><![CDATA[
53 Visualize and Interact with Principal Coordinates Analysis Plots
54 ################################################################
55
56 Generates an interactive ordination plot where the user can visually
57 integrate sample metadata.
58
59 Parameters
60 ----------
61 pcoa : PCoAResults
62 The principal coordinates matrix to be plotted.
63 metadata : Metadata
64 The sample metadata.
65 custom_axes : List[Str], optional
66 Numeric sample metadata columns that should be included as axes in the
67 Emperor plot.
68 ignore_missing_samples : Bool, optional
69 This will suppress the error raised when the coordinates matrix
70 contains samples that are not present in the metadata. Samples without
71 metadata are included by setting all metadata values to: "This sample
72 has no metadata". This flag is only applied if at least one sample is
73 present in both the coordinates matrix and the metadata.
74
75 Returns
76 -------
77 visualization : Visualization
78 ]]></help>
79 <macros>
80 <import>qiime_citation.xml</import>
81 </macros>
82 <expand macro="qiime_citation"/>
83 </tool>