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comparison qiime2/qiime_diversity_core-metrics.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 core-metrics 8 qiime diversity core-metrics
9 9
10 --i-table=$itable 10 --i-table=$itable
11 --p-sampling-depth="$psamplingdepth" 11
12 #if str($psamplingdepth):
13 --p-sampling-depth="$psamplingdepth"
14 #end if
12 15
13 #set $pnjobs = '${GALAXY_SLOTS:-4}' 16 #set $pnjobs = '${GALAXY_SLOTS:-4}'
14 #if str($pnjobs): 17 #if str($pnjobs):
15 --p-n-jobs="$pnjobs" 18 --p-n-jobs="$pnjobs"
16 #end if 19 #end if
17 20
21 #if $input_files_mmetadatafile:
18 #def list_dict_to_string(list_dict): 22 #def list_dict_to_string(list_dict):
19 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 23 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
20 #for d in list_dict[1:]: 24 #for d in list_dict[1:]:
21 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 25 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
22 #end for 26 #end for
23 #return $file_list 27 #return $file_list
24 #end def 28 #end def
25
26 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 29 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
27 30 #end if
28 31
29 --o-rarefied-table=orarefiedtable 32 --o-rarefied-table=orarefiedtable
30 --o-observed-otus-vector=oobservedotusvector 33 --o-observed-otus-vector=oobservedotusvector
31 --o-shannon-vector=oshannonvector 34 --o-shannon-vector=oshannonvector
32 --o-evenness-vector=oevennessvector 35 --o-evenness-vector=oevennessvector
54 ]]></command> 57 ]]></command>
55 <inputs> 58 <inputs>
56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/> 59 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
57 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/> 60 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
58 61
59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 62 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
60 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 63 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
61 </repeat> 64 </repeat>
62 65
63 </inputs> 66 </inputs>
64 <outputs> 67 <outputs>