annotate qiime2/qiime_gneiss_correlation-clustering.xml @ 9:f190567fe3f6 draft

Uploaded
author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents 370e0b6e9826
children a0a8d77a991c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 0
diff changeset
2 <tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Hierarchical clustering using feature correlation.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 0
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime gneiss correlation-clustering
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 #if $ppseudocount:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --p-pseudocount=$ppseudocount
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --o-clustering=oclustering
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 cp oclustering.qza $oclustering
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 Hierarchical clustering using feature correlation.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 ##################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 Build a bifurcating tree that represents a hierarchical clustering of
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 features. The hiearchical clustering uses Ward hierarchical clustering
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 based on the degree of proportionality between features.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 The feature table containing the samples in which the columns will be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 clustered.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 pseudocount : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 The value to add to zero counts in the feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 clustering : Hierarchy
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 A hierarchy of feature identifiers where each tip corresponds to the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 feature identifiers in the table. This tree can contain tip ids that
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 are not present in the table, but all feature ids in the table must be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 present in this tree.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 </tool>