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comparison qiime2/qiime_emperor_procrustes-plot.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 914fa4daf16a
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2019.4">
3 <description> - Visualize and Interact with a procrustes plot</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime emperor procrustes-plot
9
10 --i-reference-pcoa=$ireferencepcoa
11 --i-other-pcoa=$iotherpcoa
12
13
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($input_files_mmetadatafile)
23 #end if
24
25
26
27 #if str($pcustomaxes):
28 --p-custom-axes="$pcustomaxes"
29 #end if
30
31 #if $pignoremissingsamples:
32 --p-ignore-missing-samples
33 #end if
34
35 --o-visualization=ovisualization
36 ;
37 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
38 && cp -r out/* '$ovisualization.files_path'
39 && mv '$ovisualization.files_path/index.html' '$ovisualization'
40 ]]></command>
41 <inputs>
42 <param format="qza,no_unzip.zip" label="--i-reference-pcoa: ARTIFACT PCoAResults The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data"/>
43 <param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults The 'other' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data"/>
44 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>
45 <param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
46
47 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
48 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
49 </repeat>
50
51 </inputs>
52 <outputs>
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
54 </outputs>
55 <help><![CDATA[
56 Visualize and Interact with a procrustes plot
57 #############################################
58
59 Plot two procrustes-fitted matrices
60
61 Parameters
62 ----------
63 reference_pcoa : PCoAResults
64 The reference ordination matrix to be plotted.
65 other_pcoa : PCoAResults
66 The "other" ordination matrix to be plotted (the one that was fitted to
67 the reference).
68 metadata : Metadata
69 The sample metadata.
70 custom_axes : List[Str], optional
71 Numeric sample metadata columns that should be included as axes in the
72 Emperor plot.
73 ignore_missing_samples : Bool, optional
74 This will suppress the error raised when the coordinates matrix
75 contains samples that are not present in the metadata. Samples without
76 metadata are included by setting all metadata values to: "This sample
77 has no metadata". This flag is only applied if at least one sample is
78 present in both the coordinates matrix and the metadata.
79
80 Returns
81 -------
82 visualization : Visualization
83 ]]></help>
84 <macros>
85 <import>qiime_citation.xml</import>
86 </macros>
87 <expand macro="qiime_citation"/>
88 </tool>