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comparison qiime2/qiime_emperor_biplot.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_biplot" name="qiime emperor biplot" version="2019.7"> 2 <tool id="qiime_emperor_biplot" name="qiime emperor biplot"
3 <description> - Visualize and Interact with Principal Coordinates Analysis Biplot</description> 3 version="2020.8">
4 <requirements> 4 <description>Visualize and Interact with Principal Coordinates Analysis Biplot</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 biplot 9 qiime emperor biplot
9 10
10 --i-biplot=$ibiplot 11 --i-biplot=$ibiplot
11 12 # if $input_files_msamplemetadatafile:
12 13 # def list_dict_to_string(list_dict):
13 #if $m_sample_metadatafile: 14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #def list_dict_to_string_sample_mdata(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-sample-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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name') 18 # return $file_list
18 #end for 19 # end def
19 #return $file_list 20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
20 #end def 21 # end if
21 --m-sample-metadata-file=$list_dict_to_string_sample_mdata($m_sample_metadatafile) 22 # if $input_files_mfeaturemetadatafile:
22 #end if 23 # def list_dict_to_string(list_dict):
23 24 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
24 25 # for d in list_dict[1:]:
25 26 # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
26 #if $m_feature_metadatafile: 27 # end for
27 #def list_dict_to_string_feature_mdata(list_dict): 28 # return $file_list
28 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 29 # end def
29 #for d in list_dict[1:]: 30 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
30 #set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name') 31 # end if
31 #end for
32 #return $file_list
33 #end def
34 --m-feature-metadata-file=$list_dict_to_string_feature_mdata($m_feature_metadatafile)
35 #end if
36
37
38 32
39 #if $pignoremissingsamples: 33 #if $pignoremissingsamples:
40 --p-ignore-missing-samples 34 --p-ignore-missing-samples
41 #end if 35 #end if
42 36
43 #if str($pnumberoffeatures): 37 #if $pinvert:
44 --p-number-of-features=$pnumberoffeatures 38 --p-invert
45 #end if 39 #end if
46 40
41 --p-number-of-features=$pnumberoffeatures
42
47 --o-visualization=ovisualization 43 --o-visualization=ovisualization
44
45 #if str($examples) != 'None':
46 --examples=$examples
47 #end if
48
48 ; 49 ;
49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 50 cp odistancematrix.qza $odistancematrix
51
52 ;
53 qiime tools export ovisualization.qzv --output-path out
54 && mkdir -p '$ovisualization.files_path'
50 && cp -r out/* '$ovisualization.files_path' 55 && cp -r out/* '$ovisualization.files_path'
51 && mv '$ovisualization.files_path/index.html' '$ovisualization' 56 && mv '$ovisualization.files_path/index.html' '$ovisualization'
52 ]]></command>
53 <inputs>
54 <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/>
55 <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"/>
56 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>
57 57
58 <repeat name="m_sample_metadatafile" optional="False" title="--m-sample-metadata-file [required]"> 58 ]]></command>
59 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 59 <inputs>
60 </repeat> 60 <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties(\'biplot\') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data" />
61 <repeat name="input_files_msamplemetadatafile" optional="False" title="--m-sample-metadata-file">
62 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
63 </repeat>
64 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
65 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA... (multiple The feature metadata (useful to manipulate the arrows arguments will in the plot). be merged) [optional]" name="additional_input" optional="True" type="data" />
66 </repeat>
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="--p-invert: --p-invert: / --p-no-invert If specified, the point and arrow coordinates will be swapped. [default: False]" name="pinvert" selected="False" type="boolean" />
69 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin). [default: 5]" min="1" name="pnumberoffeatures" optional="True" type="integer" value="5" />
70 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
71
72 </inputs>
61 73
62 <repeat name="m_feature_metadatafile" optional="True" title="--m-feature-metadata-file"> 74 <outputs>
63 <param label="--m-feature-metadata-file: (multiple arguments will be merged) The feature metadata (useful to manipulate the arrows in the plot). [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 75 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
64 </repeat> 76
77 </outputs>
65 78
66 </inputs> 79 <help><![CDATA[
67 <outputs>
68 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
69 </outputs>
70 <help><![CDATA[
71 Visualize and Interact with Principal Coordinates Analysis Biplot 80 Visualize and Interact with Principal Coordinates Analysis Biplot
72 ################################################################# 81 ###############################################################
73 82
74 Generates an interactive ordination biplot where the user can visually 83 Generates an interactive ordination biplot where the user can visually
75 integrate sample and feature metadata. 84 integrate sample and feature metadata. Vectors representing the n most
85 important features are then plotted in the emperor visualization (5
86 largest, by default).
76 87
77 Parameters 88 Parameters
78 ---------- 89 ----------
79 biplot : PCoAResults % Properties('biplot') 90 biplot : PCoAResults % Properties('biplot')
80 The principal coordinates matrix to be plotted. 91 The principal coordinates matrix to be plotted.
86 This will suppress the error raised when the coordinates matrix 97 This will suppress the error raised when the coordinates matrix
87 contains samples that are not present in the metadata. Samples without 98 contains samples that are not present in the metadata. Samples without
88 metadata are included by setting all metadata values to: "This sample 99 metadata are included by setting all metadata values to: "This sample
89 has no metadata". This flag is only applied if at least one sample is 100 has no metadata". This flag is only applied if at least one sample is
90 present in both the coordinates matrix and the metadata. 101 present in both the coordinates matrix and the metadata.
102 invert : Bool, optional
103 If specified, the point and arrow coordinates will be swapped.
91 number_of_features : Int % Range(1, None), optional 104 number_of_features : Int % Range(1, None), optional
92 The number of most important features (arrows) to display in the 105 The number of most important features (arrows) to display in the
93 ordination. 106 ordination. “Importance” is calculated for each feature based on the
107 vector’s magnitude (euclidean distance from origin).
94 108
95 Returns 109 Returns
96 ------- 110 -------
97 visualization : Visualization 111 visualization : Visualization
98 ]]></help> 112 ]]></help>
99 <macros> 113 <macros>
100 <import>qiime_citation.xml</import> 114 <import>qiime_citation.xml</import>
101 </macros> 115 </macros>
102 <expand macro="qiime_citation"/> 116 <expand macro="qiime_citation"/>
103 </tool> 117 </tool>