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comparison qiime2-2020.8/qiime_composition_ancom.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
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[
9 qiime composition ancom
10
11 --i-table=$itable
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($input_files_mmetadatafile)
21 # end if
22
23 #if '__ob__' in str($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 = $mmetadatacolumn_temp
42 #end if
43
44 --m-metadata-column=$mmetadatacolumn
45
46
47 #if str($ptransformfunction) != 'None':
48 --p-transform-function=$ptransformfunction
49 #end if
50
51 #if str($pdifferencefunction) != 'None':
52 --p-difference-function=$pdifferencefunction
53 #end if
54
55 --o-visualization=ovisualization
56
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'
67 && cp -r out/* '$ovisualization.files_path'
68 && mv '$ovisualization.files_path/index.html' '$ovisualization'
69
70 ]]></command>
71 <inputs>
72 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
73 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
74 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
75 </repeat>
76 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text" />
77 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
78 <option selected="True" value="None">Selection is Optional</option>
79 <option value="sqrt">sqrt</option>
80 <option value="log">log</option>
81 <option value="clr">clr</option>
82 </param>
83 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
84 <option selected="True" value="None">Selection is Optional</option>
85 <option value="mean_difference">mean_difference</option>
86 <option value="f_statistic">f_statistic</option>
87 </param>
88 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
89
90 </inputs>
91
92 <outputs>
93 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
94
95 </outputs>
96
97 <help><![CDATA[
98 Apply ANCOM to identify features that differ in abundance.
99 ###############################################################
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
121 ]]></help>
122 <macros>
123 <import>qiime_citation.xml</import>
124 </macros>
125 <expand macro="qiime_citation"/>
126 </tool>