|
0
|
1 <?xml version="1.0" ?>
|
|
14
|
2 <tool id="qiime_composition_ancom" name="qiime composition ancom"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Apply ANCOM to identify features that differ in abundance.</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
0
|
9 qiime composition ancom
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
14
|
12 # if $input_files_mmetadatafile:
|
|
|
13 # def list_dict_to_string(list_dict):
|
|
|
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
15 # for d in list_dict[1:]:
|
|
|
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
17 # end for
|
|
|
18 # return $file_list
|
|
|
19 # end def
|
|
|
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
21 # end if
|
|
6
|
22
|
|
14
|
23 #if '__ob__' in str($mmetadatacolumn):
|
|
|
24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
|
|
|
25 #set $mmetadatacolumn = $mmetadatacolumn_temp
|
|
|
26 #end if
|
|
|
27 #if '__cb__' in str($mmetadatacolumn):
|
|
|
28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
|
|
|
29 #set $mmetadatacolumn = $mmetadatacolumn_temp
|
|
|
30 #end if
|
|
|
31 #if 'X' in str($mmetadatacolumn):
|
|
|
32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
|
|
|
33 #set $mmetadatacolumn = $mmetadatacolumn_temp
|
|
|
34 #end if
|
|
|
35 #if '__sq__' in str($mmetadatacolumn):
|
|
|
36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
|
|
|
37 #set $mmetadatacolumn = $mmetadatacolumn_temp
|
|
|
38 #end if
|
|
|
39 #if '__db__' in str($mmetadatacolumn):
|
|
|
40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
|
|
|
41 #set $mmetadatacolumn = $mmetadatacolumn_temp
|
|
2
|
42 #end if
|
|
0
|
43
|
|
14
|
44 --m-metadata-column=$mmetadatacolumn
|
|
0
|
45
|
|
|
46
|
|
|
47 #if str($ptransformfunction) != 'None':
|
|
|
48 --p-transform-function=$ptransformfunction
|
|
|
49 #end if
|
|
|
50
|
|
14
|
51 #if str($pdifferencefunction) != 'None':
|
|
|
52 --p-difference-function=$pdifferencefunction
|
|
|
53 #end if
|
|
|
54
|
|
|
55 --o-visualization=ovisualization
|
|
0
|
56
|
|
14
|
57 #if str($examples) != 'None':
|
|
|
58 --examples=$examples
|
|
|
59 #end if
|
|
|
60
|
|
|
61 ;
|
|
|
62 cp ocompositiontable.qza $ocompositiontable
|
|
|
63
|
|
|
64 ;
|
|
|
65 qiime tools export ovisualization.qzv --output-path out
|
|
|
66 && mkdir -p '$ovisualization.files_path'
|
|
0
|
67 && cp -r out/* '$ovisualization.files_path'
|
|
|
68 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
6
|
69
|
|
14
|
70 ]]></command>
|
|
|
71 <inputs>
|
|
|
72 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
|
|
|
73 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
|
74 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
|
|
|
75 </repeat>
|
|
|
76 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text" />
|
|
|
77 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
|
|
|
78 <option selected="True" value="None">Selection is Optional</option>
|
|
|
79 <option value="sqrt">sqrt</option>
|
|
|
80 <option value="log">log</option>
|
|
|
81 <option value="clr">clr</option>
|
|
|
82 </param>
|
|
|
83 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
|
|
|
84 <option selected="True" value="None">Selection is Optional</option>
|
|
|
85 <option value="mean_difference">mean_difference</option>
|
|
|
86 <option value="f_statistic">f_statistic</option>
|
|
|
87 </param>
|
|
|
88 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
89
|
|
|
90 </inputs>
|
|
|
91
|
|
|
92 <outputs>
|
|
|
93 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
94
|
|
|
95 </outputs>
|
|
|
96
|
|
|
97 <help><![CDATA[
|
|
0
|
98 Apply ANCOM to identify features that differ in abundance.
|
|
14
|
99 ###############################################################
|
|
0
|
100
|
|
|
101 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
|
|
|
102 that are differentially abundant across groups.
|
|
|
103
|
|
|
104 Parameters
|
|
|
105 ----------
|
|
|
106 table : FeatureTable[Composition]
|
|
|
107 The feature table to be used for ANCOM computation.
|
|
|
108 metadata : MetadataColumn[Categorical]
|
|
|
109 The categorical sample metadata column to test for differential
|
|
|
110 abundance across.
|
|
|
111 transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
|
|
|
112 The method applied to transform feature values before generating
|
|
|
113 volcano plots.
|
|
|
114 difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
|
|
|
115 The method applied to visualize fold difference in feature abundances
|
|
|
116 across groups for volcano plots.
|
|
|
117
|
|
|
118 Returns
|
|
|
119 -------
|
|
|
120 visualization : Visualization
|
|
14
|
121 ]]></help>
|
|
|
122 <macros>
|
|
0
|
123 <import>qiime_citation.xml</import>
|
|
14
|
124 </macros>
|
|
|
125 <expand macro="qiime_citation"/>
|
|
|
126 </tool> |
