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comparison qiime2/qiime_gneiss_gradient-clustering.xml @ 9:f190567fe3f6 draft

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author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents 51025741f326
children a0a8d77a991c
comparison
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8:d66c7509e8f9 9:f190567fe3f6
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.4"> 2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.7">
3 <description> - Hierarchical clustering using gradient information.</description> 3 <description> - Hierarchical clustering using gradient information.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.7">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime gneiss gradient-clustering 8 qiime gneiss gradient-clustering
9 9
10 --i-table=$itable 10 --i-table=$itable
11 --m-gradient-column="$mgradientcolumn" 11 --m-gradient-column="$mgradientcolumn"
12 12
13 13
14 #if $input_files_mgradientfile: 14 #if $mgradientfile:
15 #def list_dict_to_string(list_dict): 15 --m-gradient-file=$mgradientfile
16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 #for d in list_dict[1:]:
18 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
19 #end for
20 #return $file_list
21 #end def
22 --m-gradient-file=$list_dict_to_string($input_files_mgradientfile)
23 #end if 16 #end if
24 17
25 #if $pnoweighted: 18 #if $pnoweighted:
26 --p-no-weighted 19 --p-no-weighted
27 #end if 20 #end if
33 <inputs> 26 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/> 27 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/>
35 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/> 28 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/>
36 <param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/> 29 <param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/>
37 30
38 <repeat name="input_files_mgradientfile" optional="False" title="--m-gradient-file"> 31 <param label="--m-gradient-file: " name="mgradientfile" optional="True" type="data" format="tabular,qza,no_unzip.zip" />
39 <param label="--m-gradient-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
40 </repeat>
41 32
42 </inputs> 33 </inputs>
43 <outputs> 34 <outputs>
44 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/> 35 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/>
45 </outputs> 36 </outputs>