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comparison qiime2/qiime_composition_ancom.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_composition_ancom" name="qiime composition ancom" version="2018.4">
3 <description> - Apply ANCOM to identify features that differ in abundance.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime composition ancom --i-table=$itable
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
20
21 #if str($pdifferencefunction) != 'None':
22 --p-difference-function=$pdifferencefunction
23 #end if
24
25 #if str($cmdconfig) != 'None':
26 --cmd-config=$cmdconfig
27 #end if
28
29 #if str($ptransformfunction) != 'None':
30 --p-transform-function=$ptransformfunction
31 #end if
32
33 --o-visualization=ovisualization;
34
35 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
36 && cp -r out/* '$ovisualization.files_path'
37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
38
39 ]]></command>
40 <inputs>
41 <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"/>
42 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
43 <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"/>
44 </repeat>
45 <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"/>
46 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
47 <option selected="True" value="None">Selection is Optional</option>
48 <option value="mean_difference">mean_difference</option>
49 <option value="f_statistic">f_statistic</option>
50 </param>
51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
52 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="log">log</option>
55 <option value="clr">clr</option>
56 <option value="sqrt">sqrt</option>
57 </param>
58 </inputs>
59 <outputs>
60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
61 </outputs>
62 <help>
63 <![CDATA[
64 Apply ANCOM to identify features that differ in abundance.
65 ----------------------------------------------------------
66
67 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
68 that are differentially abundant across groups.
69
70 Parameters
71 ----------
72 table : FeatureTable[Composition]
73 The feature table to be used for ANCOM computation.
74 metadata : MetadataColumn[Categorical]
75 The categorical sample metadata column to test for differential
76 abundance across.
77 transform_function : Str % Choices({'clr', 'log', 'sqrt'}), optional
78 The method applied to transform feature values before generating
79 volcano plots.
80 difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional
81 The method applied to visualize fold difference in feature abundances
82 across groups for volcano plots.
83
84 Returns
85 -------
86 visualization : Visualization
87
88 ]]>
89 </help>
90 <macros>
91 <import>qiime_citation.xml</import>
92 </macros>
93 <expand macro="qiime_citation" />
94 </tool>