comparison qiime2/qiime_diversity_alpha-group-significance.xml @ 6:de4c22a52df4 draft

Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
12 12
13 #if $input_files_mmetadatafile: 13 #if $input_files_mmetadatafile:
14 #def list_dict_to_string(list_dict): 14 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]: 16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for 18 #end for
19 #return $file_list 19 #return $file_list
20 #end def 20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if 22 #end if
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
40 </outputs> 40 </outputs>
41 <help><![CDATA[ 41 <help><![CDATA[
42 Beta diversity group significance 42 Alpha diversity comparisons
43 #################################
44 43
45 Determine whether groups of samples are significantly different from one 44 Visually and statistically compare groups of alpha diversity values.
46 another using a permutation-based statistical test.
47 45
48 Parameters 46 Parameters
49 ---------- 47 ----------
50 distance_matrix : DistanceMatrix 48 alpha_diversity : SampleData[AlphaDiversity]
51 Matrix of distances between pairs of samples. 49 Vector of alpha diversity values by sample.
52 metadata : MetadataColumn[Categorical] 50 metadata : Metadata
53 Categorical sample metadata column. 51 The sample metadata.
54 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
55 The group significance test to be applied.
56 pairwise : Bool, optional
57 Perform pairwise tests between all pairs of groups in addition to the
58 test across all groups. This can be very slow if there are a lot of
59 groups in the metadata column.
60 permutations : Int, optional
61 The number of permutations to be run when computing p-values.
62 52
63 Returns 53 Returns
64 ------- 54 -------
65 visualization : Visualization 55 visualization : Visualization
66 ]]></help> 56 ]]></help>