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comparison qiime2/qiime_composition_ancom.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.4">
3 <description> - Apply ANCOM to identify features that differ in abundance.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime composition ancom
9
10 --i-table=$itable
11
12 #def list_dict_to_string(list_dict):
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #for d in list_dict[1:]:
15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
16 #end for
17 #return $file_list
18 #end def
19
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
21
22 #if str($pdifferencefunction) != 'None':
23 --p-difference-function=$pdifferencefunction
24 #end if
25
26 #if str($ptransformfunction) != 'None':
27 --p-transform-function=$ptransformfunction
28 #end if
29
30 --o-visualization=ovisualization;
31
32 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
33 && cp -r out/* '$ovisualization.files_path'
34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
35 ]]></command>
36 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] - The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data"/>
38 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
39 <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
40 </repeat>
41 <param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text"/>
42 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
43 <option selected="True" value="None">Selection is Optional</option>
44 <option value="mean_difference">mean_difference</option>
45 <option value="f_statistic">f_statistic</option>
46 </param>
47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
48 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
49 <option selected="True" value="None">Selection is Optional</option>
50 <option value="log">log</option>
51 <option value="clr">clr</option>
52 <option value="sqrt">sqrt</option>
53 </param>
54 </inputs>
55 <outputs>
56 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
57 </outputs>
58 <help><![CDATA[
59 Apply ANCOM to identify features that differ in abundance.
60 ##########################################################
61
62 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
63 that are differentially abundant across groups.
64
65 Parameters
66 ----------
67 table : FeatureTable[Composition]
68 The feature table to be used for ANCOM computation.
69 metadata : MetadataColumn[Categorical]
70 The categorical sample metadata column to test for differential
71 abundance across.
72 transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
73 The method applied to transform feature values before generating
74 volcano plots.
75 difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
76 The method applied to visualize fold difference in feature abundances
77 across groups for volcano plots.
78
79 Returns
80 -------
81 visualization : Visualization
82 ]]></help>
83 <macros>
84 <import>qiime_citation.xml</import>
85 </macros>
86 <expand macro="qiime_citation"/>
87 </tool>