Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_diversity_beta-rarefaction.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 51025741f326
children de4c22a52df4
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
30 30
31 #if $input_files_mmetadatafile: 31 #if $input_files_mmetadatafile:
32 #def list_dict_to_string(list_dict): 32 #def list_dict_to_string(list_dict):
33 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 33 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
34 #for d in list_dict[1:]: 34 #for d in list_dict[1:]:
35 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 35 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
36 #end for 36 #end for
37 #return $file_list 37 #return $file_list
38 #end def 38 #end def
39 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 39 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
40 #end if 40 #end if
41 41
42 --o-visualization=ovisualization 42 --o-visualization=ovisualization
43 ; 43 ;
44 cp mmetadatafile.qza $mmetadatafile;
45 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 44 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
46 && cp -r out/* '$ovisualization.files_path' 45 && cp -r out/* '$ovisualization.files_path'
47 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 46 && mv '$ovisualization.files_path/index.html' '$ovisualization';
48 ]]></command> 47 ]]></command>
49 <inputs> 48 <inputs>
107 <option value="RdYlBu_r">RdYlBu_r</option> 106 <option value="RdYlBu_r">RdYlBu_r</option>
108 <option value="RdYlGn">RdYlGn</option> 107 <option value="RdYlGn">RdYlGn</option>
109 <option value="RdYlGn_r">RdYlGn_r</option> 108 <option value="RdYlGn_r">RdYlGn_r</option>
110 </param> 109 </param>
111 110
112 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 111 <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" /> 112 <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> 113 </repeat>
115 114
116 </inputs> 115 </inputs>
117 <outputs> 116 <outputs>