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comparison qiime2/qiime_diversity_beta-rarefaction.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
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime diversity beta-rarefaction 8 qiime diversity beta-rarefaction
9 9
10 --i-table=$itable 10 --i-table=$itable
11
11 --p-metric=$pmetric 12 --p-metric=$pmetric
13
12 --p-clustering-method=$pclusteringmethod 14 --p-clustering-method=$pclusteringmethod
13 --p-sampling-depth="$psamplingdepth" 15
16 #if str($psamplingdepth):
17 --p-sampling-depth="$psamplingdepth"
18 #end if
14 19
15 #if str($iphylogeny) != 'None': 20 #if str($iphylogeny) != 'None':
16 --i-phylogeny=$iphylogeny 21 --i-phylogeny=$iphylogeny
17 #end if 22 #end if
18 23
19 #if $piterations: 24 #if str($piterations):
20 --p-iterations=$piterations 25 --p-iterations=$piterations
21 #end if 26 #end if
22 27
23 #if str($pcorrelationmethod) != 'None': 28 #if str($pcorrelationmethod) != 'None':
24 --p-correlation-method=$pcorrelationmethod 29 --p-correlation-method=$pcorrelationmethod
26 31
27 #if str($pcolorscheme) != 'None': 32 #if str($pcolorscheme) != 'None':
28 --p-color-scheme=$pcolorscheme 33 --p-color-scheme=$pcolorscheme
29 #end if 34 #end if
30 35
36 #if $input_files_mmetadatafile:
31 #def list_dict_to_string(list_dict): 37 #def list_dict_to_string(list_dict):
32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
33 #for d in list_dict[1:]: 39 #for d in list_dict[1:]:
34 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
35 #end for 41 #end for
36 #return $file_list 42 #return $file_list
37 #end def 43 #end def
38
39 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
40 45 #end if
41 46
42 --o-visualization=ovisualization 47 --o-visualization=ovisualization
43 ; 48 ;
44 cp mmetadatafile.qza $mmetadatafile;
45 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
46 && cp -r out/* '$ovisualization.files_path' 50 && cp -r out/* '$ovisualization.files_path'
47 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 51 && mv '$ovisualization.files_path/index.html' '$ovisualization';
48 ]]></command> 52 ]]></command>
49 <inputs> 53 <inputs>
107 <option value="RdYlBu_r">RdYlBu_r</option> 111 <option value="RdYlBu_r">RdYlBu_r</option>
108 <option value="RdYlGn">RdYlGn</option> 112 <option value="RdYlGn">RdYlGn</option>
109 <option value="RdYlGn_r">RdYlGn_r</option> 113 <option value="RdYlGn_r">RdYlGn_r</option>
110 </param> 114 </param>
111 115
112 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 116 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
113 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 117 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
114 </repeat> 118 </repeat>
115 119
116 </inputs> 120 </inputs>
117 <outputs> 121 <outputs>