Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_emperor_procrustes-plot.xml @ 0:51b9b6b57732 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:51b9b6b57732
1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2018.4">
3 <description> - Visualize and Interact with a procrustes plot</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime emperor procrustes-plot --i-reference-pcoa=$ireferencepcoa
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($input_files_mmetadatafile) --i-other-pcoa=$iotherpcoa
19
20 #if str($pcustomaxes):
21 --p-custom-axes="$pcustomaxes"
22 #end if
23
24 #if str($cmdconfig) != 'None':
25 --cmd-config=$cmdconfig
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-reference-pcoa: PCoAResults The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data"/>
36 <param format="qza,no_unzip.zip" label="--i-other-pcoa: PCoAResults The 'other' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data"/>
37
38 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
39 <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" />
40
41 </repeat>
42
43 <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"/>
44
45 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
46 </inputs>
47 <outputs>
48 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
49 </outputs>
50 <help><![CDATA[
51 Visualize and Interact with a procrustes plot
52 ----------------------------------------------
53
54 Plot two procrustes-fitted matrices
55
56 Parameters
57 ----------
58 reference_pcoa : PCoAResults
59 The reference ordination matrix to be plotted.
60 other_pcoa : PCoAResults
61 The "other" ordination matrix to be plotted (the one that was fitted to
62 the reference).
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
69 Returns
70 -------
71 visualization : Visualization
72 \
73 ]]>
74 </help>
75 <macros>
76 <import>qiime_citation.xml</import>
77 </macros>
78 <expand macro="qiime_citation" />
79 </tool>