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comparison qiime2/qiime_diversity_beta-correlation.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
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3:eda5df31da55 4:71f124e02000
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime diversity beta-correlation 8 qiime diversity beta-correlation
9 9
10 --i-distance-matrix=$idistancematrix 10 --i-distance-matrix=$idistancematrix
11
12
13
14 #if '__sq__' in str($mmetadatacolumn):
15 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
16 #set $mmetadatacolumn = $mmetadatacolumn_temp
17 #end if
18
11 --m-metadata-column="$mmetadatacolumn" 19 --m-metadata-column="$mmetadatacolumn"
20
21
12 22
13 #if str($pmethod) != 'None': 23 #if str($pmethod) != 'None':
14 --p-method=$pmethod 24 --p-method=$pmethod
15 #end if 25 #end if
16 26
17 #if $ppermutations: 27 #if str($ppermutations):
18 --p-permutations=$ppermutations 28 --p-permutations=$ppermutations
19 #end if 29 #end if
20 30
21 #if $pintersectids: 31 #if str($pintersectids):
22 --p-intersect-ids 32 --p-intersect-ids
33 #end if
34
35
36
37
38 #if '__sq__' in str($plabel1):
39 #set $plabel1_temp = $plabel1.replace('__sq__', "'")
40 #set $plabel1 = $plabel1_temp
23 #end if 41 #end if
24 42
25 #if str($plabel1): 43 #if str($plabel1):
26 --p-label1="$plabel1" 44 --p-label1="$plabel1"
27 #end if 45 #end if
28 46
47
48
49 #if '__sq__' in str($plabel2):
50 #set $plabel2_temp = $plabel2.replace('__sq__', "'")
51 #set $plabel2 = $plabel2_temp
52 #end if
53
29 #if str($plabel2): 54 #if str($plabel2):
30 --p-label2="$plabel2" 55 --p-label2="$plabel2"
31 #end if 56 #end if
32 57
33 #if $input_files_mmetadatafile: 58
34 #def list_dict_to_string(list_dict): 59
35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 60 #if $metadatafile:
36 #for d in list_dict[1:]: 61 --m-metadata-file=$metadatafile
37 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
38 #end for
39 #return $file_list
40 #end def
41 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
42 #end if 62 #end if
63
64
65
43 66
44 --o-metadata-distance-matrix=ometadatadistancematrix 67 --o-metadata-distance-matrix=ometadatadistancematrix
45 --o-mantel-scatter-visualization=omantelscattervisualization 68 --o-mantel-scatter-visualization=omantelscattervisualization
46 ; 69 ;
47 cp ometadatadistancematrix.qza $ometadatadistancematrix; 70 cp ometadatadistancematrix.qza $ometadatadistancematrix;
57 <option value="spearman">spearman</option> 80 <option value="spearman">spearman</option>
58 <option value="pearson">pearson</option> 81 <option value="pearson">pearson</option>
59 </param> 82 </param>
60 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/> 83 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
61 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/> 84 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
62 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="'Metadata'"/> 85 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/>
63 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="'Distance Matrix'"/> 86 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/>
64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 87
65 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 88 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
66 </repeat> 89
67 </inputs> 90 </inputs>
68 <outputs> 91 <outputs>
69 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/> 92 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
70 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/> 93 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
71 </outputs> 94 </outputs>