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comparison qiime_gneiss_balance-taxonomy.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2018.4">
3 <description>- Balance Summary</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime gneiss balance-taxonomy --i-tree=$itree --p-balance-name="$pbalancename"
10
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
13 --i-taxonomy '$tax'
14 #else:
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
16 --i-taxonomy '$tax'
17 #end if
18
19 --i-table=$itable
20 #if $pnfeatures:
21 --p-n-features=$pnfeatures
22 #end if
23
24 #if str($mmetadatacolumn):
25 --m-metadata-column="$mmetadatacolumn"
26 #end if
27
28 #if str($cmdconfig) != 'None':
29 --cmd-config=$cmdconfig
30 #end if
31
32 #if $ptaxalevel:
33 --p-taxa-level=$ptaxalevel
34 #end if
35 --o-visualization=ovisualization
36 #if $input_files_mmetadatafile:
37
38 #def list_dict_to_string(list_dict):
39 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
40 #for d in list_dict[1:]:
41 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
42 #end for
43 #return $file_list
44 #end def
45 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
46 #end if
47
48 #if str($pthreshold):
49 --p-threshold="$pthreshold"
50 #end if
51 ;
52 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
53 && cp -r out/* '$ovisualization.files_path'
54 && mv '$ovisualization.files_path/index.html' '$ovisualization'
55 ]]>
56 </command>
57 <inputs>
58 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] A table of compositions. [required]" name="itable" optional="False" type="data"/>
59 <param format="qza,no_unzip.zip" label="--i-tree: Hierarchy The tree used to calculate the balances. [required]" name="itree" optional="False" type="data"/>
60
61 <conditional name="id_to_taxonomy_fp" optional="True">
62 <param name="selector" type="select" label="Reference taxonomy to query">
63 <option value="cached">Public databases</option>
64 <option value="history">Databases from your history</option>
65 </param>
66 <when value="cached">
67 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
68 <options from_data_table="qiime_taxonomy" />
69 </param>
70 </when>
71 <when value="history">
72 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
73 </when>
74 </conditional>
75
76 <param label="--p-balance-name: Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/>
77 <param label="--p-taxa-level: Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/>
78 <param label="--p-n-features: The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/>
79 <param label="--p-threshold: 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="text"/>
80
81 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
82 <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" />
83 </repeat>
84 <param label="--m-metadata-column: MetadataColumn[Categorical | Numeric] Column from metadata file or artifact viewable as metadata. Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/>
85
86 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
87 </inputs>
88 <outputs>
89 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
90 </outputs>
91 <help>
92 <![CDATA[
93 Balance Summary
94 ----------------
95
96 Visualize the distribution of a single balance and summarize its numerator
97 and denominator components.
98
99 Parameters
100 ----------
101 table : FeatureTable[Composition]
102 A table of compositions.
103 tree : Hierarchy
104 The tree used to calculate the balances.
105 taxonomy : FeatureData[Taxonomy]
106 Taxonomy information for the OTUs.
107 balance_name : Str
108 Name of the balance to summarize.
109 taxa_level : Int, optional
110 Level of taxonomy to summarize.
111 n_features : Int, optional
112 The number of features to plot in the proportion plot.
113 threshold : Float, optional
114 A threshold to designate discrete categories for a numerical metadata
115 column. This will split the numerical column values into two
116 categories, values below the threshold, and values above the threshold.
117 If not specified, this threshold will default to the mean.
118 metadata : MetadataColumn[Categorical | Numeric], optional
119 Metadata column for plotting the balance (optional).
120
121 Returns
122 -------
123 visualization : Visualization
124 \
125 ]]>
126 </help>
127 </tool>