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comparison qiime2/qiime_gneiss_balance-taxonomy.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children de4c22a52df4
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-1:000000000000 0:370e0b6e9826
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>