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comparison qiime2/qiime_gneiss_gradient-clustering.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2018.4">
3 <description> - Hierarchical clustering using gradient information.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime gneiss gradient-clustering --i-table=$itable --m-gradient-column="$mgradientcolumn"
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-gradient-file=$list_dict_to_string($input_files_mgradientfile)
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 #if $pweighted:
25 --p-weighted
26 #else
27 --p-no-weighted
28 #end if
29
30 --o-clustering=oclustering;
31 cp oclustering.qza $oclustering;
32 ]]>
33 </command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition | Frequency | RelativeFrequency] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/>
36 <param label="--m-gradient-column: MetadataColumn[Numeric] Column from metadata file or artifact viewable as metadata. Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/>
37
38 <repeat name="input_files_mgradientfile" optional="False" title="--m-gradient-file">
39 <param label="--m-gradient-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
40 </repeat>
41
42 <param label="--p-weighted: --p-no-weighted Specifies if abundance or presence/absence information should be used to perform the clustering. [default: True]" name="pweighted" checked="True" type="boolean"/>
43 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
44 </inputs>
45 <outputs>
46 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/>
47 </outputs>
48 <help>
49 <![CDATA[
50 Hierarchical clustering using gradient information.
51 ----------------------------------------------------
52
53 Build a bifurcating tree that represents a hierarchical clustering of
54 features. The hiearchical clustering uses Ward hierarchical clustering
55 based on the mean difference of gradients that each feature is observed in.
56 This method is primarily used to sort the table to reveal the underlying
57 block-like structures.
58
59 Parameters
60 ----------
61 table : FeatureTable[Composition | Frequency | RelativeFrequency]
62 The feature table containing the samples in which the columns will be
63 clustered.
64 gradient : MetadataColumn[Numeric]
65 Contains gradient values to sort the features and samples.
66 weighted : Bool, optional
67 Specifies if abundance or presence/absence information should be used
68 to perform the clustering.
69
70 Returns
71 -------
72 clustering : Hierarchy
73 A hierarchy of feature identifiers where each tipcorresponds to the
74 feature identifiers in the table. This tree can contain tip ids that
75 are not present in the table, but all feature ids in the table must be
76 present in this tree.
77 ]]>
78 </help>
79 <macros>
80 <import>qiime_citation.xml</import>
81 </macros>
82 <expand macro="qiime_citation" />
83 </tool>