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comparison qiime2/qiime_diversity_core-metrics-phylogenetic.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
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime diversity core-metrics-phylogenetic 8 qiime diversity core-metrics-phylogenetic
9 9
10 --i-table=$itable 10 --i-table=$itable
11 --i-phylogeny=$iphylogeny 11 --i-phylogeny=$iphylogeny
12 --p-sampling-depth="$psamplingdepth" 12
13 #if str($psamplingdepth):
14 --p-sampling-depth="$psamplingdepth"
15 #end if
13 16
14 #set $pnjobs = '${GALAXY_SLOTS:-4}' 17 #set $pnjobs = '${GALAXY_SLOTS:-4}'
15 #if str($pnjobs): 18 #if str($pnjobs):
16 --p-n-jobs="$pnjobs" 19 --p-n-jobs="$pnjobs"
17 #end if 20 #end if
18 21
22
23 #if $input_files_mmetadatafile:
19 #def list_dict_to_string(list_dict): 24 #def list_dict_to_string(list_dict):
20 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
21 #for d in list_dict[1:]: 26 #for d in list_dict[1:]:
22 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 27 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
23 #end for 28 #end for
24 #return $file_list 29 #return $file_list
25 #end def 30 #end def
31 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
32 #end if
26 33
27 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
28 34
29 35
30 --o-rarefied-table=orarefiedtable 36 --o-rarefied-table=orarefiedtable
31 --o-faith-pd-vector=ofaithpdvector 37 --o-faith-pd-vector=ofaithpdvector
32 --o-observed-otus-vector=oobservedotusvector 38 --o-observed-otus-vector=oobservedotusvector
74 <inputs> 80 <inputs>
75 <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"/> 81 <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"/>
76 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/> 82 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/>
77 <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"/> 83 <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"/>
78 84
79 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 85 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
80 <param label="--m-metadata-file: (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" /> 86 <param label="--m-metadata-file: (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" type="data" format="tabular,qza,no_unzip.zip" />
81 </repeat> 87 </repeat>
82 88
83 </inputs> 89 </inputs>
84 <outputs> 90 <outputs>
85 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/> 91 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>