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comparison qiime2/qiime_emperor_plot.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_emperor_plot" name="qiime emperor plot" version="2019.7"> 2 <tool id="qiime_emperor_plot" name="qiime emperor plot"
3 <description> - Visualize and Interact with Principal Coordinates Analysis Plots</description> 3 version="2020.8">
4 <requirements> 4 <description>Visualize and Interact with Principal Coordinates Analysis Plots</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime emperor plot 9 qiime emperor plot
9 10
10 --i-pcoa=$ipcoa 11 --i-pcoa=$ipcoa
11 12 # if $input_files_mmetadatafile:
12 13 # def list_dict_to_string(list_dict):
13 #if $input_files_mmetadatafile: 14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #def list_dict_to_string(list_dict): 15 # for d in list_dict[1:]:
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]: 17 # end for
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') 18 # return $file_list
18 #end for 19 # end def
19 #return $file_list 20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
20 #end def 21 # end if
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if
23
24 22
25 #if str($pcustomaxes): 23 #if str($pcustomaxes):
26 --p-custom-axes="$pcustomaxes" 24 --p-custom-axes=$pcustomaxes
27 #end if 25 #end if
28
29 #if $pignoremissingsamples: 26 #if $pignoremissingsamples:
30 --p-ignore-missing-samples 27 --p-ignore-missing-samples
31 #end if 28 #end if
32 29
33 --o-visualization=ovisualization 30 --o-visualization=ovisualization
31
32 #if str($examples) != 'None':
33 --examples=$examples
34 #end if
35
34 ; 36 ;
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 37 cp odistancematrix.qza $odistancematrix
38
39 ;
40 qiime tools export ovisualization.qzv --output-path out
41 && mkdir -p '$ovisualization.files_path'
36 && cp -r out/* '$ovisualization.files_path' 42 && cp -r out/* '$ovisualization.files_path'
37 && mv '$ovisualization.files_path/index.html' '$ovisualization' 43 && 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
44 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 45 ;
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 qiime tools export ovisualization.qzv --output-path out
46 </repeat> 47 && mkdir -p '$ovisualization.files_path'
48 && cp -r out/* '$ovisualization.files_path'
49 && mv '$ovisualization.files_path/index.html' '$ovisualization'
47 50
48 </inputs> 51 ]]></command>
49 <outputs> 52 <inputs>
50 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 53 <param format="qza,no_unzip.zip" label="--i-pcoa: ARTIFACT The principal coordinates matrix to be plotted. PCoAResults [required]" name="ipcoa" optional="False" type="data" />
51 </outputs> 54 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
52 <help><![CDATA[ 55 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
56 </repeat>
57 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="False" type="text" />
58 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
65
66 </outputs>
67
68 <help><![CDATA[
53 Visualize and Interact with Principal Coordinates Analysis Plots 69 Visualize and Interact with Principal Coordinates Analysis Plots
54 ################################################################ 70 ###############################################################
55 71
56 Generates an interactive ordination plot where the user can visually 72 Generates an interactive ordination plot where the user can visually
57 integrate sample metadata. 73 integrate sample metadata.
58 74
59 Parameters 75 Parameters
73 present in both the coordinates matrix and the metadata. 89 present in both the coordinates matrix and the metadata.
74 90
75 Returns 91 Returns
76 ------- 92 -------
77 visualization : Visualization 93 visualization : Visualization
78 ]]></help> 94 ]]></help>
79 <macros> 95 <macros>
80 <import>qiime_citation.xml</import> 96 <import>qiime_citation.xml</import>
81 </macros> 97 </macros>
82 <expand macro="qiime_citation"/> 98 <expand macro="qiime_citation"/>
83 </tool> 99 </tool>