annotate qiime2-2020.8/qiime_gneiss_gradient-clustering.xml @ 25:499916460746 draft

Deleted selected files
author florianbegusch
date Fri, 04 Sep 2020 12:56:26 +0000
parents d93d8888f0b0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering"
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
3 version="2020.8">
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
4 <description>Hierarchical clustering using gradient information.</description>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
5 <requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
7 </requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
8 <command><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
9 qiime gneiss gradient-clustering
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
10
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
11 --i-table=$itable
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
12
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
13 #if str($mgradientfile) != 'None':
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
14 --m-gradient-file=$mgradientfile
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
15 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
16
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
17 #if '__ob__' in str($mgradientcolumn):
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
18 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__ob__', '[')
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
19 #set $mgradientcolumn = $mgradientcolumn_temp
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
20 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
21 #if '__cb__' in str($mgradientcolumn):
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
22 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__cb__', ']')
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
23 #set $mgradientcolumn = $mgradientcolumn_temp
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
24 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
25 #if 'X' in str($mgradientcolumn):
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
26 #set $mgradientcolumn_temp = $mgradientcolumn.replace('X', '\\')
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
27 #set $mgradientcolumn = $mgradientcolumn_temp
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
28 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
29 #if '__sq__' in str($mgradientcolumn):
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
30 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__sq__', "'")
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
31 #set $mgradientcolumn = $mgradientcolumn_temp
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
32 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
33 #if '__db__' in str($mgradientcolumn):
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
34 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__db__', '"')
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
35 #set $mgradientcolumn = $mgradientcolumn_temp
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
36 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
37
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
38 --m-gradient-column=$mgradientcolumn
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
39
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
40
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
41 #if $pignoremissingsamples:
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
42 --p-ignore-missing-samples
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
43 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
44
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
45 #if $pnoweighted:
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
46 --p-no-weighted
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
47 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
48
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
49 --o-clustering=oclustering
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
50
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
51 #if str($examples) != 'None':
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
52 --examples=$examples
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
53 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
54
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
55 ;
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
56 cp oclustering.qza $oclustering
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
57
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
58 ]]></command>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
59 <inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
60 <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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
61 <param format="tabular,qza,no_unzip.zip" label="--m-gradient-file: METADATA" name="mgradientfile" optional="False" type="data" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
62 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
63 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
64 <param label="--p-no-weighted: Do not specifies if abundance or presence/absence information should be used to perform the clustering. [default: True]" name="pnoweighted" selected="False" type="boolean" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
66
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
67 </inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
68
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
69 <outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
70 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
71
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
72 </outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
73
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
74 <help><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
75 Hierarchical clustering using gradient information.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
76 ###############################################################
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
77
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
78 Build a bifurcating tree that represents a hierarchical clustering of
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
79 features. The hiearchical clustering uses Ward hierarchical clustering
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
80 based on the mean difference of gradients that each feature is observed in.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
81 This method is primarily used to sort the table to reveal the underlying
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
82 block-like structures.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
83
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
84 Parameters
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
85 ----------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
86 table : FeatureTable[Frequency | RelativeFrequency | Composition]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
87 The feature table containing the samples in which the columns will be
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
88 clustered.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
89 gradient : MetadataColumn[Numeric]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
90 Contains gradient values to sort the features and samples.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
91 ignore_missing_samples : Bool, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
92 weighted : Bool, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
93 Specifies if abundance or presence/absence information should be used
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
94 to perform the clustering.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
95
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
96 Returns
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
97 -------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
98 clustering : Hierarchy
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
99 A hierarchy of feature identifiers where each tip corresponds to the
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
100 feature identifiers in the table. This tree can contain tip ids that
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
101 are not present in the table, but all feature ids in the table must be
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
102 present in this tree.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
103 ]]></help>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
104 <macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
105 <import>qiime_citation.xml</import>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
106 </macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
107 <expand macro="qiime_citation"/>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
108 </tool>