|
0
|
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 </tool>
|
