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comparison qiime2/qiime_gneiss_gradient-clustering.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.7"> 2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering"
3 <description> - Hierarchical clustering using gradient information.</description> 3 version="2020.8">
4 <requirements> 4 <description>Hierarchical clustering using gradient information.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime gneiss gradient-clustering 9 qiime gneiss gradient-clustering
9 10
10 --i-table=$itable 11 --i-table=$itable
11 --m-gradient-column="$mgradientcolumn" 12
13 #if str($mgradientfile) != 'None':
14 --m-gradient-file=$mgradientfile
15 #end if
16
17 #if '__ob__' in str($mgradientcolumn):
18 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__ob__', '[')
19 #set $mgradientcolumn = $mgradientcolumn_temp
20 #end if
21 #if '__cb__' in str($mgradientcolumn):
22 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__cb__', ']')
23 #set $mgradientcolumn = $mgradientcolumn_temp
24 #end if
25 #if 'X' in str($mgradientcolumn):
26 #set $mgradientcolumn_temp = $mgradientcolumn.replace('X', '\\')
27 #set $mgradientcolumn = $mgradientcolumn_temp
28 #end if
29 #if '__sq__' in str($mgradientcolumn):
30 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__sq__', "'")
31 #set $mgradientcolumn = $mgradientcolumn_temp
32 #end if
33 #if '__db__' in str($mgradientcolumn):
34 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__db__', '"')
35 #set $mgradientcolumn = $mgradientcolumn_temp
36 #end if
37
38 --m-gradient-column=$mgradientcolumn
12 39
13 40
14 #if $mgradientfile: 41 #if $pignoremissingsamples:
15 --m-gradient-file=$mgradientfile 42 --p-ignore-missing-samples
16 #end if 43 #end if
17 44
18 #if $pnoweighted: 45 #if $pnoweighted:
19 --p-no-weighted 46 --p-no-weighted
20 #end if 47 #end if
21 48
22 --o-clustering=oclustering 49 --o-clustering=oclustering
50
51 #if str($examples) != 'None':
52 --examples=$examples
53 #end if
54
23 ; 55 ;
24 cp oclustering.qza $oclustering 56 cp oclustering.qza $oclustering
25 ]]></command>
26 <inputs>
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"/>
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"/>
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"/>
30 57
31 <param label="--m-gradient-file: " name="mgradientfile" optional="True" type="data" format="tabular,qza,no_unzip.zip" /> 58 ]]></command>
59 <inputs>
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" />
61 <param format="tabular,qza,no_unzip.zip" label="--m-gradient-file: METADATA" name="mgradientfile" optional="False" type="data" />
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" />
63 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
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" />
65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
66
67 </inputs>
32 68
33 </inputs> 69 <outputs>
34 <outputs> 70 <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"/> 71
36 </outputs> 72 </outputs>
37 <help><![CDATA[ 73
74 <help><![CDATA[
38 Hierarchical clustering using gradient information. 75 Hierarchical clustering using gradient information.
39 ################################################### 76 ###############################################################
40 77
41 Build a bifurcating tree that represents a hierarchical clustering of 78 Build a bifurcating tree that represents a hierarchical clustering of
42 features. The hiearchical clustering uses Ward hierarchical clustering 79 features. The hiearchical clustering uses Ward hierarchical clustering
43 based on the mean difference of gradients that each feature is observed in. 80 based on the mean difference of gradients that each feature is observed in.
44 This method is primarily used to sort the table to reveal the underlying 81 This method is primarily used to sort the table to reveal the underlying
49 table : FeatureTable[Frequency | RelativeFrequency | Composition] 86 table : FeatureTable[Frequency | RelativeFrequency | Composition]
50 The feature table containing the samples in which the columns will be 87 The feature table containing the samples in which the columns will be
51 clustered. 88 clustered.
52 gradient : MetadataColumn[Numeric] 89 gradient : MetadataColumn[Numeric]
53 Contains gradient values to sort the features and samples. 90 Contains gradient values to sort the features and samples.
91 ignore_missing_samples : Bool, optional
54 weighted : Bool, optional 92 weighted : Bool, optional
55 Specifies if abundance or presence/absence information should be used 93 Specifies if abundance or presence/absence information should be used
56 to perform the clustering. 94 to perform the clustering.
57 95
58 Returns 96 Returns
60 clustering : Hierarchy 98 clustering : Hierarchy
61 A hierarchy of feature identifiers where each tip corresponds to the 99 A hierarchy of feature identifiers where each tip corresponds to the
62 feature identifiers in the table. This tree can contain tip ids that 100 feature identifiers in the table. This tree can contain tip ids that
63 are not present in the table, but all feature ids in the table must be 101 are not present in the table, but all feature ids in the table must be
64 present in this tree. 102 present in this tree.
65 ]]></help> 103 ]]></help>
66 <macros> 104 <macros>
67 <import>qiime_citation.xml</import> 105 <import>qiime_citation.xml</import>
68 </macros> 106 </macros>
69 <expand macro="qiime_citation"/> 107 <expand macro="qiime_citation"/>
70 </tool> 108 </tool>