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comparison qiime2/qiime_diversity_bioenv.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_diversity_bioenv" name="qiime diversity bioenv" version="2019.7"> 2 <tool id="qiime_diversity_bioenv" name="qiime diversity bioenv"
3 <description> - bioenv</description> 3 version="2020.8">
4 <requirements> 4 <description>bioenv</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 diversity bioenv 9 qiime diversity bioenv
9 10
10 --i-distance-matrix=$idistancematrix 11 --i-distance-matrix=$idistancematrix
12 # if $input_files_mmetadatafile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
11 22
23 --o-visualization=ovisualization
12 24
13 #if $input_files_mmetadatafile: 25 #if str($examples) != 'None':
14 #def list_dict_to_string(list_dict): 26 --examples=$examples
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if 27 #end if
23 28
29 ;
30 cp odistancematrix.qza $odistancematrix
24 31
25 --o-visualization=ovisualization
26 ; 32 ;
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 33 qiime tools export ovisualization.qzv --output-path out
34 && mkdir -p '$ovisualization.files_path'
28 && cp -r out/* '$ovisualization.files_path' 35 && cp -r out/* '$ovisualization.files_path'
29 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
30 ]]></command>
31 <inputs>
32 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
33 37
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 38 ;
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 39 qiime tools export ovisualization.qzv --output-path out
36 </repeat> 40 && mkdir -p '$ovisualization.files_path'
41 && cp -r out/* '$ovisualization.files_path'
42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37 43
38 </inputs> 44 ]]></command>
39 <outputs> 45 <inputs>
40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 46 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
41 </outputs> 47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
42 <help><![CDATA[ 48 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
49 </repeat>
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
51
52 </inputs>
53
54 <outputs>
55 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
56
57 </outputs>
58
59 <help><![CDATA[
43 bioenv 60 bioenv
44 ###### 61 ###############################################################
45 62
46 Find the subsets of variables in metadata whose Euclidean distances are 63 Find the subsets of variables in metadata whose Euclidean distances are
47 maximally rank-correlated with distance matrix. All numeric variables in 64 maximally rank-correlated with distance matrix. All numeric variables in
48 metadata will be considered, and samples which are missing data will be 65 metadata will be considered, and samples which are missing data will be
49 dropped. The output visualization will indicate how many samples were 66 dropped. The output visualization will indicate how many samples were
57 The sample metadata. 74 The sample metadata.
58 75
59 Returns 76 Returns
60 ------- 77 -------
61 visualization : Visualization 78 visualization : Visualization
62 ]]></help> 79 ]]></help>
63 <macros> 80 <macros>
64 <import>qiime_citation.xml</import> 81 <import>qiime_citation.xml</import>
65 </macros> 82 </macros>
66 <expand macro="qiime_citation"/> 83 <expand macro="qiime_citation"/>
67 </tool> 84 </tool>