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comparison qiime2/qiime_diversity_mantel.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
12 12
13 #if str($pmethod) != 'None': 13 #if str($pmethod) != 'None':
14 --p-method=$pmethod 14 --p-method=$pmethod
15 #end if 15 #end if
16 16
17 #if $ppermutations: 17 #if str($ppermutations):
18 --p-permutations=$ppermutations 18 --p-permutations=$ppermutations
19 #end if 19 #end if
20 20
21 #if $pintersectids: 21 #if $pintersectids:
22 --p-intersect-ids 22 --p-intersect-ids
23 #end if 23 #end if
24 24
25
26
27 #if '__sq__' in str($plabel1):
28 #set $plabel1_temp = $plabel1.replace('__sq__', "'")
29 #set $plabel1 = $plabel1_temp
30 #end if
31
25 #if str($plabel1): 32 #if str($plabel1):
26 --p-label1="$plabel1" 33 --p-label1="$plabel1"
34 #end if
35
36
37
38 #if '__sq__' in str($plabel2):
39 #set $plabel2_temp = $plabel2.replace('__sq__', "'")
40 #set $plabel2 = $plabel2_temp
27 #end if 41 #end if
28 42
29 #if str($plabel2): 43 #if str($plabel2):
30 --p-label2="$plabel2" 44 --p-label2="$plabel2"
31 #end if 45 #end if
46
47
32 48
33 --o-visualization=ovisualization 49 --o-visualization=ovisualization
34 ; 50 ;
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
36 && cp -r out/* '$ovisualization.files_path' 52 && cp -r out/* '$ovisualization.files_path'
44 <option value="spearman">spearman</option> 60 <option value="spearman">spearman</option>
45 <option value="pearson">pearson</option> 61 <option value="pearson">pearson</option>
46 </param> 62 </param>
47 <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"/> 63 <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"/>
48 <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"/> 64 <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"/>
49 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="'Distance Matrix 1'"/> 65 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
50 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="'Distance Matrix 2'"/> 66 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
51 </inputs> 67 </inputs>
52 <outputs> 68 <outputs>
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 69 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
54 </outputs> 70 </outputs>
55 <help><![CDATA[ 71 <help><![CDATA[