annotate qiime2/qiime_diversity_alpha-group-significance.xml @ 2:51025741f326 draft

Uploaded
author florianbegusch
date Thu, 18 Jul 2019 12:19:15 -0400
parents 370e0b6e9826
children 914fa4daf16a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Alpha diversity comparisons</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime diversity alpha-group-significance
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-alpha-diversity=$ialphadiversity
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
2
51025741f326 Uploaded
florianbegusch
parents: 0
diff changeset
13 #if $input_files_mmetadatafile:
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #def list_dict_to_string(list_dict):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #for d in list_dict[1:]:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #end for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #return $file_list
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end def
2
51025741f326 Uploaded
florianbegusch
parents: 0
diff changeset
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
51025741f326 Uploaded
florianbegusch
parents: 0
diff changeset
22 #end if
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 </repeat>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 Beta diversity group significance
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 #################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 Determine whether groups of samples are significantly different from one
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 another using a permutation-based statistical test.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 distance_matrix : DistanceMatrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 Matrix of distances between pairs of samples.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 metadata : MetadataColumn[Categorical]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 Categorical sample metadata column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 The group significance test to be applied.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 pairwise : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 Perform pairwise tests between all pairs of groups in addition to the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 test across all groups. This can be very slow if there are a lot of
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 groups in the metadata column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 permutations : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 The number of permutations to be run when computing p-values.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 </tool>