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comparison qiime2-2020.8/qiime_emperor_procrustes-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_procrustes-plot" name="qiime emperor procrustes-plot"
3 version="2020.8">
4 <description>Visualize and Interact with a procrustes plot</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime emperor procrustes-plot
10
11 --i-reference-pcoa=$ireferencepcoa
12
13 --i-other-pcoa=$iotherpcoa
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 #if str($pcustomaxes):
26 --p-custom-axes=$pcustomaxes
27 #end if
28 #if $pignoremissingsamples:
29 --p-ignore-missing-samples
30 #end if
31
32 --o-visualization=ovisualization
33
34 #if str($examples) != 'None':
35 --examples=$examples
36 #end if
37
38 ;
39 cp odistancematrix.qza $odistancematrix
40
41 ;
42 qiime tools export ovisualization.qzv --output-path out
43 && mkdir -p '$ovisualization.files_path'
44 && cp -r out/* '$ovisualization.files_path'
45 && mv '$ovisualization.files_path/index.html' '$ovisualization'
46
47 ;
48 qiime tools export ovisualization.qzv --output-path out
49 && mkdir -p '$ovisualization.files_path'
50 && cp -r out/* '$ovisualization.files_path'
51 && mv '$ovisualization.files_path/index.html' '$ovisualization'
52
53 ;
54 qiime tools export ovisualization.qzv --output-path out
55 && mkdir -p '$ovisualization.files_path'
56 && cp -r out/* '$ovisualization.files_path'
57 && mv '$ovisualization.files_path/index.html' '$ovisualization'
58
59 ]]></command>
60 <inputs>
61 <param format="qza,no_unzip.zip" label="--i-reference-pcoa: ARTIFACT PCoAResults The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data" />
62 <param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults The \'other\' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data" />
63 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
64 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
65 </repeat>
66 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="False" type="text" />
67 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
68 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
69
70 </inputs>
71
72 <outputs>
73 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
74
75 </outputs>
76
77 <help><![CDATA[
78 Visualize and Interact with a procrustes plot
79 ###############################################################
80
81 Plot two procrustes-fitted matrices
82
83 Parameters
84 ----------
85 reference_pcoa : PCoAResults
86 The reference ordination matrix to be plotted.
87 other_pcoa : PCoAResults
88 The "other" ordination matrix to be plotted (the one that was fitted to
89 the reference).
90 metadata : Metadata
91 The sample metadata.
92 custom_axes : List[Str], optional
93 Numeric sample metadata columns that should be included as axes in the
94 Emperor plot.
95 ignore_missing_samples : Bool, optional
96 This will suppress the error raised when the coordinates matrix
97 contains samples that are not present in the metadata. Samples without
98 metadata are included by setting all metadata values to: "This sample
99 has no metadata". This flag is only applied if at least one sample is
100 present in both the coordinates matrix and the metadata.
101
102 Returns
103 -------
104 visualization : Visualization
105 ]]></help>
106 <macros>
107 <import>qiime_citation.xml</import>
108 </macros>
109 <expand macro="qiime_citation"/>
110 </tool>