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comparison qiime2/qiime_diversity_adonis.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
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3:eda5df31da55 4:71f124e02000
8 qiime diversity adonis 8 qiime diversity adonis
9 9
10 --i-distance-matrix=$idistancematrix 10 --i-distance-matrix=$idistancematrix
11 11
12 12
13 #if $input_files_mmetadatafile:
13 #def list_dict_to_string(list_dict): 14 #def list_dict_to_string(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]: 16 #for d in list_dict[1:]:
16 #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')
17 #end for 18 #end for
18 #return $file_list 19 #return $file_list
19 #end def 20 #end def
20 21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 --m-metadata-file=$list_dict_to_string("$input_files_mmetadatafile") 22 #end if
22 23
23 24
24 25
26 #if '__sq__' in str($pformula):
27 #set $pformula_temp = $pformula.replace('__sq__', "'")
28 #set $pformula = $pformula_temp
29 #end if
25 30
26 --p-formula="$pformula" 31 --p-formula="$pformula"
27 32
28 #if $ppermutations: 33
34
35 #if str($ppermutations):
29 --p-permutations=$ppermutations 36 --p-permutations=$ppermutations
30 #end if 37 #end if
31 38
32 #set $pnjobs = '${GALAXY_SLOTS:-4}' 39 #set $pnjobs = '${GALAXY_SLOTS:-4}'
33 #if str($pnjobs): 40 #if str($pnjobs):
43 <inputs> 50 <inputs>
44 <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"/> 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"/>
45 <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"/> 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"/>
46 <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"/> 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"/>
47 54
48 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 55 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
49 <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"/> 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"/>
50 </repeat> 57 </repeat>
51 </inputs> 58 </inputs>
52 <outputs> 59 <outputs>
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>