|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2019.4">
|
|
|
3 <description> - Balance Summary</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime gneiss balance-taxonomy
|
|
|
9
|
|
|
10 --i-table=$itable
|
|
|
11 --i-tree=$itree
|
|
|
12 --i-taxonomy=$itaxonomy
|
|
|
13 --p-balance-name="$pbalancename"
|
|
|
14
|
|
|
15
|
|
|
16 #if $input_files_mmetadatafile:
|
|
|
17 #def list_dict_to_string(list_dict):
|
|
|
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
19 #for d in list_dict[1:]:
|
|
|
20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
21 #end for
|
|
|
22 #return $file_list
|
|
|
23 #end def
|
|
|
24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
25 #end if
|
|
|
26
|
|
|
27
|
|
|
28 #if $ppseudocount:
|
|
|
29 --p-pseudocount=$ppseudocount
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #if $ptaxalevel:
|
|
|
33 --p-taxa-level=$ptaxalevel
|
|
|
34 #end if
|
|
|
35
|
|
|
36 #if $pnfeatures:
|
|
|
37 --p-n-features=$pnfeatures
|
|
|
38 #end if
|
|
|
39
|
|
|
40 #if str($pthreshold):
|
|
|
41 --p-threshold="$pthreshold"
|
|
|
42 #end if
|
|
|
43 #if str($mmetadatacolumn):
|
|
|
44 --m-metadata-column="$mmetadatacolumn"
|
|
|
45 #end if
|
|
|
46
|
|
|
47 --o-visualization=ovisualization
|
|
|
48 ;
|
|
|
49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
50 && cp -r out/* '$ovisualization.files_path'
|
|
|
51 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
52 ]]></command>
|
|
|
53 <inputs>
|
|
|
54 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A table of abundances. [required]" name="itable" optional="False" type="data"/>
|
|
|
55 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree used to calculate the balances. Hierarchy [required]" name="itree" optional="False" type="data"/>
|
|
|
56 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomy information for the OTUs. [required]" name="itaxonomy" optional="False" type="data"/>
|
|
|
57 <param label="--p-balance-name: TEXT Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/>
|
|
|
58 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
|
|
|
59 <param label="--p-taxa-level: INTEGER Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/>
|
|
|
60 <param label="--p-n-features: INTEGER The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/>
|
|
|
61 <param label="--p-threshold: NUMBER A threshold to designate discrete categories for a numerical metadata column. This will split the numerical column values into two categories, values below the threshold, and values above the threshold. If not specified, this threshold will default to the mean. [optional]" name="pthreshold" optional="True" type="float"/>
|
|
|
62 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical | Numeric] Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/>
|
|
|
63
|
|
|
64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
|
65 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
66 </repeat>
|
|
|
67
|
|
|
68 </inputs>
|
|
|
69 <outputs>
|
|
|
70 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
71 </outputs>
|
|
|
72 <help><![CDATA[
|
|
|
73 Balance Summary
|
|
|
74 ###############
|
|
|
75
|
|
|
76 Visualize the distribution of a single balance and summarize its numerator
|
|
|
77 and denominator components.
|
|
|
78
|
|
|
79 Parameters
|
|
|
80 ----------
|
|
|
81 table : FeatureTable[Frequency]
|
|
|
82 A table of abundances.
|
|
|
83 tree : Hierarchy
|
|
|
84 The tree used to calculate the balances.
|
|
|
85 taxonomy : FeatureData[Taxonomy]
|
|
|
86 Taxonomy information for the OTUs.
|
|
|
87 balance_name : Str
|
|
|
88 Name of the balance to summarize.
|
|
|
89 pseudocount : Float, optional
|
|
|
90 The pseudocount to add to avoid division by zero.
|
|
|
91 taxa_level : Int, optional
|
|
|
92 Level of taxonomy to summarize.
|
|
|
93 n_features : Int, optional
|
|
|
94 The number of features to plot in the proportion plot.
|
|
|
95 threshold : Float, optional
|
|
|
96 A threshold to designate discrete categories for a numerical metadata
|
|
|
97 column. This will split the numerical column values into two
|
|
|
98 categories, values below the threshold, and values above the threshold.
|
|
|
99 If not specified, this threshold will default to the mean.
|
|
|
100 metadata : MetadataColumn[Categorical | Numeric], optional
|
|
|
101 Metadata column for plotting the balance (optional).
|
|
|
102
|
|
|
103 Returns
|
|
|
104 -------
|
|
|
105 visualization : Visualization
|
|
|
106 ]]></help>
|
|
|
107 <macros>
|
|
|
108 <import>qiime_citation.xml</import>
|
|
|
109 </macros>
|
|
|
110 <expand macro="qiime_citation"/>
|
|
|
111 </tool>
|
