|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.7">
|
|
0
|
3 <description> - Group samples or features by a metadata column</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime feature-table group
|
|
|
9
|
|
|
10 --i-table=$itable
|
|
|
11 --p-axis=$paxis
|
|
|
12 --m-metadata-column="$mmetadatacolumn"
|
|
|
13 --p-mode=$pmode
|
|
|
14
|
|
|
15
|
|
4
|
16 --m-metadata-file=$mmedatafile
|
|
0
|
17
|
|
|
18 --o-grouped-table=ogroupedtable
|
|
|
19 ;
|
|
|
20 cp ogroupedtable.qza $ogroupedtable
|
|
|
21 ]]></command>
|
|
|
22 <inputs>
|
|
|
23 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data"/>
|
|
|
24 <param label="--p-axis: " name="paxis" optional="False" type="select">
|
|
|
25 <option value="feature">feature</option>
|
|
|
26 <option value="sample">sample</option>
|
|
|
27 </param>
|
|
|
28 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] A column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text"/>
|
|
|
29 <param label="--p-mode: " name="pmode" optional="False" type="select">
|
|
|
30 <option value="median-ceiling">median-ceiling</option>
|
|
|
31 <option value="mean-ceiling">mean-ceiling</option>
|
|
|
32 <option value="sum">sum</option>
|
|
|
33 </param>
|
|
|
34
|
|
4
|
35 <param label="--m-metadata-file [required]" name="mmedatafile" type="data" format="tabular,qza,no_unzip.zip" />
|
|
0
|
36
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable"/>
|
|
|
40 </outputs>
|
|
|
41 <help><![CDATA[
|
|
|
42 Group samples or features by a metadata column
|
|
|
43 ##############################################
|
|
|
44
|
|
|
45 Group samples or features in a feature table using metadata to define the
|
|
|
46 mapping of IDs to a group.
|
|
|
47
|
|
|
48 Parameters
|
|
|
49 ----------
|
|
|
50 table : FeatureTable[Frequency]
|
|
|
51 The table to group samples or features on.
|
|
|
52 axis : Str % Choices('sample', 'feature')
|
|
|
53 Along which axis to group. Each ID in the given axis must exist in
|
|
|
54 `metadata`.
|
|
|
55 metadata : MetadataColumn[Categorical]
|
|
|
56 A column defining the groups. Each unique value will become a new ID
|
|
|
57 for the table on the given `axis`.
|
|
|
58 mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
|
|
|
59 How to combine samples or features within a group. `sum` will sum the
|
|
|
60 frequencies across all samples or features within a group; `mean-
|
|
|
61 ceiling` will take the ceiling of the mean of these frequencies;
|
|
|
62 `median-ceiling` will take the ceiling of the median of these
|
|
|
63 frequencies.
|
|
|
64
|
|
|
65 Returns
|
|
|
66 -------
|
|
|
67 grouped_table : FeatureTable[Frequency]
|
|
|
68 A table that has been grouped along the given `axis`. IDs on that axis
|
|
|
69 are replaced by values in the `metadata` column.
|
|
|
70 ]]></help>
|
|
|
71 <macros>
|
|
|
72 <import>qiime_citation.xml</import>
|
|
|
73 </macros>
|
|
|
74 <expand macro="qiime_citation"/>
|
|
|
75 </tool>
|
