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comparison qiime2/qiime_emperor_plot.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_plot" name="qiime emperor plot" version="2018.4">
3 <description> - Visualize and Interact with Principal Coordinates Analysis Plots</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime emperor plot
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-pcoa=$ipcoa
19
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 #if str($pcustomaxes):
25 --p-custom-axes="$pcustomaxes"
26 #end if
27
28 --o-visualization=ovisualization;
29
30 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
31 && cp -r out/* '$ovisualization.files_path'
32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
33 ]]></command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-pcoa: PCoAResults The principal coordinates matrix to be plotted. [required]" name="ipcoa" optional="False" type="data"/>
36 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
37 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
38 </repeat>
39 <param label="--p-custom-axes: Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>
40 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
41 </inputs>
42 <outputs>
43 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
44 </outputs>
45 <help><![CDATA[
46 Visualize and Interact with Principal Coordinates Analysis Plots
47 ----------------------------------------------------------------
48
49 Generate visualization of your ordination.
50
51 Parameters
52 ----------
53 pcoa : PCoAResults
54 The principal coordinates matrix to be plotted.
55 metadata : Metadata
56 The sample metadata.
57 custom_axes : List[Str], optional
58 Numeric sample metadata columns that should be included as axes in the
59 Emperor plot.
60
61 Returns
62 -------
63 visualization : Visualization
64 \
65 ]]>
66 </help>
67 <macros>
68 <import>qiime_citation.xml</import>
69 </macros>
70 <expand macro="qiime_citation" />
71 </tool>