annotate qiime2/qiime_longitudinal_plot-feature-volatility.xml @ 10:21c7954105a9 draft

Fix
author florianbegusch
date Sun, 25 Aug 2019 10:26:27 -0400
parents f190567fe3f6
children a0a8d77a991c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
2 <tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Plot longitudinal feature volatility and importances</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime longitudinal plot-feature-volatility
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-importances=$iimportances
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-state-column="$pstatecolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
4
florianbegusch
parents: 0
diff changeset
14
florianbegusch
parents: 0
diff changeset
15
florianbegusch
parents: 0
diff changeset
16 #if '__sq__' in str($pindividualidcolumn):
florianbegusch
parents: 0
diff changeset
17 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
florianbegusch
parents: 0
diff changeset
18 #set $pindividualidcolumn = $pindividualidcolumn_temp
florianbegusch
parents: 0
diff changeset
19 #end if
florianbegusch
parents: 0
diff changeset
20
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 #if str($pindividualidcolumn):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 --p-individual-id-column="$pindividualidcolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
4
florianbegusch
parents: 0
diff changeset
25
florianbegusch
parents: 0
diff changeset
26
florianbegusch
parents: 0
diff changeset
27
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 #if str($pdefaultgroupcolumn):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 --p-default-group-column="$pdefaultgroupcolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 #if str($pyscale) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 --p-yscale=$pyscale
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 #if $input_files_mmetadatafile:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 #def list_dict_to_string(list_dict):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 #for d in list_dict[1:]:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 #end for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 #return $file_list
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 #end def
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 && mv '$ovisualization.files_path/index.html' '$ovisualization'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="True" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 <option value="linear">linear</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 <option value="pow">pow</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 <option value="sqrt">sqrt</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 <option value="log">log</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68
4
florianbegusch
parents: 0
diff changeset
69 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <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" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 </repeat>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 Plot longitudinal feature volatility and importances
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 ####################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 Plots an interactive control chart of feature abundances (y-axis) in each
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 sample across time (or state; x-axis). Feature importance scores and
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 descriptive statistics for each each feature are plotted in interactive bar
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 charts below the control chart, facilitating exploration of longitudinal
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 feature data. This visualization is intended for use with the feature-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 volatility pipeline; use that pipeline to access this visualization.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 table : FeatureTable[RelativeFrequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 Feature table containing features found in importances.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 importances : FeatureData[Importance]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 Feature importance scores.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 metadata : Metadata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 Sample metadata file containing individual_id_column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 state_column : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 Metadata column containing state (time) variable information.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 individual_id_column : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 Metadata column containing IDs for individual subjects.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 default_group_column : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 The default metadata column on which to separate groups for comparison
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 (all categorical metadata columns will be available in the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 visualization).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 y-axis scaling strategy to apply.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
108 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
110 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
111 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
112 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
113 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
114 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
115 </tool>