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comparison qiime2/qiime_diversity_adonis.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_adonis" name="qiime diversity adonis" version="2019.7"> 2 <tool id="qiime_diversity_adonis" name="qiime diversity adonis"
3 <description> - adonis PERMANOVA test for beta group significance</description> 3 version="2020.8">
4 <requirements> 4 <description>adonis PERMANOVA test for beta group significance</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 adonis 9 qiime diversity adonis
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($input_files_mmetadatafile)
21 # end if
11 22
23 --p-formula=$pformula
12 24
13 #if $input_files_mmetadatafile: 25 --p-permutations=$ppermutations
14 #def list_dict_to_string(list_dict): 26
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 27 --p-n-jobs=$pnjobs
16 #for d in list_dict[1:]: 28
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') 29 --o-visualization=ovisualization
18 #end for 30
19 #return $file_list 31 #if str($examples) != 'None':
20 #end def 32 --examples=$examples
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if 33 #end if
23 34
35 ;
36 cp osubsampledsequences.qza $osubsampledsequences
24 37
25
26 #if '__sq__' in str($pformula):
27 #set $pformula_temp = $pformula.replace('__sq__', "'")
28 #set $pformula = $pformula_temp
29 #end if
30
31 --p-formula="$pformula"
32
33
34
35 #if str($ppermutations):
36 --p-permutations=$ppermutations
37 #end if
38
39 #set $pnjobs = '${GALAXY_SLOTS:-4}'
40 #if str($pnjobs):
41 --p-n-jobs="$pnjobs"
42 #end if
43
44 --o-visualization=ovisualization
45 ; 38 ;
46 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 39 qiime tools export ovisualization.qzv --output-path out
40 && mkdir -p '$ovisualization.files_path'
47 && cp -r out/* '$ovisualization.files_path' 41 && cp -r out/* '$ovisualization.files_path'
48 && mv '$ovisualization.files_path/index.html' '$ovisualization' 42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
49 ]]></command>
50 <inputs>
51 <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"/>
52 <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text"/>
53 <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
54 43
55 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> 44 ;
56 <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/> 45 qiime tools export ovisualization.qzv --output-path out
57 </repeat> 46 && mkdir -p '$ovisualization.files_path'
58 </inputs> 47 && cp -r out/* '$ovisualization.files_path'
59 <outputs> 48 && mv '$ovisualization.files_path/index.html' '$ovisualization'
60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 49
61 </outputs> 50 ]]></command>
62 <help><![CDATA[ 51 <inputs>
52 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
53 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
54 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
55 </repeat>
56 <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text" />
57 <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" />
58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
59
60 </inputs>
61
62 <outputs>
63 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
64
65 </outputs>
66
67 <help><![CDATA[
63 adonis PERMANOVA test for beta group significance 68 adonis PERMANOVA test for beta group significance
64 ################################################## 69 ###############################################################
65 70
66 Determine whether groups of samples are significantly different from one 71 Determine whether groups of samples are significantly different from one
67 another using the ADONIS permutation-based statistical test in vegan-R. The 72 another using the ADONIS permutation-based statistical test in vegan-R. The
68 function partitions sums of squares of a multivariate data set, and is 73 function partitions sums of squares of a multivariate data set, and is
69 directly analogous to MANOVA (multivariate analysis of variance). This 74 directly analogous to MANOVA (multivariate analysis of variance). This
87 formula "treatment*block" would test both of those effects as well as 92 formula "treatment*block" would test both of those effects as well as
88 their interaction. Enclose formulae in quotes to avoid unpleasant 93 their interaction. Enclose formulae in quotes to avoid unpleasant
89 surprises. 94 surprises.
90 permutations : Int % Range(1, None), optional 95 permutations : Int % Range(1, None), optional
91 The number of permutations to be run when computing p-values. 96 The number of permutations to be run when computing p-values.
97 n_jobs : Int % Range(1, None), optional
98 Number of parallel processes to run.
92 99
93 Returns 100 Returns
94 ------- 101 -------
95 visualization : Visualization 102 visualization : Visualization
96 ]]></help> 103 ]]></help>
97 <macros> 104 <macros>
98 <import>qiime_citation.xml</import> 105 <import>qiime_citation.xml</import>
99 </macros> 106 </macros>
100 <expand macro="qiime_citation"/> 107 <expand macro="qiime_citation"/>
101 </tool> 108 </tool>