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comparison qiime2/qiime_diversity_alpha-rarefaction.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime diversity alpha-rarefaction 8 qiime diversity alpha-rarefaction
9 9
10 --i-table=$itable 10 --i-table=$itable
11 --p-max-depth="$pmaxdepth" 11
12
13 #if str($pmaxdepth):
14 --p-max-depth="$pmaxdepth"
15 #end if
12 16
13 #if str($iphylogeny) != 'None': 17 #if str($iphylogeny) != 'None':
14 --i-phylogeny=$iphylogeny 18 --i-phylogeny=$iphylogeny
15 #end if 19 #end if
16 20
17 #if str($pmetrics) != 'None': 21 #if str($pmetrics) != 'None':
18 --p-metrics=$pmetrics 22 --p-metrics=$pmetrics
19 #end if 23 #end if
20 24
21 25
22 #if $pmindepth: 26 #if str($pmindepth):
23 --p-min-depth=$pmindepth 27 --p-min-depth=$pmindepth
24 #end if 28 #end if
25 29
26 #if $psteps: 30 #if str($psteps):
27 --p-steps=$psteps 31 --p-steps=$psteps
28 #end if 32 #end if
29 33
30 #if $piterations: 34 #if str($piterations):
31 --p-iterations=$piterations 35 --p-iterations=$piterations
32 #end if 36 #end if
33 37
34 #if $input_files_mmetadatafile: 38 #if $input_files_mmetadatafile:
35 #def list_dict_to_string(list_dict): 39 #def list_dict_to_string(list_dict):
36 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 40 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
37 #for d in list_dict[1:]: 41 #for d in list_dict[1:]:
38 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 42 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
39 #end for 43 #end for
40 #return $file_list 44 #return $file_list
41 #end def 45 #end def
42 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 46 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
43 #end if 47 #end if