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comparison qiime2/qiime_diversity_alpha-correlation.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_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.7"> 2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation"
3 <description> - Alpha diversity correlation</description> 3 version="2020.8">
4 <requirements> 4 <description>Alpha diversity correlation</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 alpha-correlation 9 qiime diversity alpha-correlation
9 10
10 --i-alpha-diversity=$ialphadiversity 11 --i-alpha-diversity=$ialphadiversity
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
12 #if $input_files_mmetadatafile: 23 #if str($pmethod) != 'None':
13 #def list_dict_to_string(list_dict): 24 --p-method=$pmethod
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($input_files_mmetadatafile)
21 #end if 25 #end if
22 26
23 #if str($pmethod) != 'None': 27 #if $pintersectids:
24 --p-method=$pmethod 28 --p-intersect-ids
25 #end if 29 #end if
26 30
27 --o-visualization=ovisualization 31 --o-visualization=ovisualization
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
28 ; 37 ;
29 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 38 cp oalphadiversity.qza $oalphadiversity
39
40 ;
41 qiime tools export ovisualization.qzv --output-path out
42 && mkdir -p '$ovisualization.files_path'
30 && cp -r out/* '$ovisualization.files_path' 43 && cp -r out/* '$ovisualization.files_path'
31 && mv '$ovisualization.files_path/index.html' '$ovisualization' 44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
32 ]]></command>
33 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
35 <param label="--p-method: " name="pmethod" optional="True" type="select">
36 <option selected="True" value="None">Selection is Optional</option>
37 <option value="spearman">spearman</option>
38 <option value="pearson">pearson</option>
39 </param>
40 45
41 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 46 ]]></command>
42 <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" /> 47 <inputs>
43 </repeat> 48 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" />
44 </inputs> 49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
45 <outputs> 50 <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" />
46 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 51 </repeat>
47 </outputs> 52 <param label="--p-method: " name="pmethod" optional="True" type="select">
48 <help><![CDATA[ 53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="spearman">spearman</option>
55 <option value="pearson">pearson</option>
56 </param>
57 <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" />
58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
59
60 </inputs>
61
62 <outputs>
63 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
64
65 </outputs>
66
67 <help><![CDATA[
49 Alpha diversity correlation 68 Alpha diversity correlation
50 ########################### 69 ###############################################################
51 70
52 Determine whether numeric sample metadata columns are correlated with alpha 71 Determine whether numeric sample metadata columns are correlated with alpha
53 diversity. 72 diversity.
54 73
55 Parameters 74 Parameters
58 Vector of alpha diversity values by sample. 77 Vector of alpha diversity values by sample.
59 metadata : Metadata 78 metadata : Metadata
60 The sample metadata. 79 The sample metadata.
61 method : Str % Choices('spearman', 'pearson'), optional 80 method : Str % Choices('spearman', 'pearson'), optional
62 The correlation test to be applied. 81 The correlation test to be applied.
82 intersect_ids : Bool, optional
83 If supplied, IDs that are not found in both the alpha diversity vector
84 and metadata will be discarded before calculating the correlation.
85 Default behavior is to error on any mismatched IDs.
63 86
64 Returns 87 Returns
65 ------- 88 -------
66 visualization : Visualization 89 visualization : Visualization
67 ]]></help> 90 ]]></help>
68 <macros> 91 <macros>
69 <import>qiime_citation.xml</import> 92 <import>qiime_citation.xml</import>
70 </macros> 93 </macros>
71 <expand macro="qiime_citation"/> 94 <expand macro="qiime_citation"/>
72 </tool> 95 </tool>