annotate qiime2/qiime_feature-table_group.xml @ 12:33e7a3470046 draft

Deleted selected files
author florianbegusch
date Thu, 03 Sep 2020 09:44:28 +0000
parents f190567fe3f6
children a0a8d77a991c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
2 <tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Group samples or features by a metadata column</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime feature-table group
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --p-axis=$paxis
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --m-metadata-column="$mmetadatacolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --p-mode=$pmode
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15
4
florianbegusch
parents: 0
diff changeset
16 --m-metadata-file=$mmedatafile
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 --o-grouped-table=ogroupedtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 cp ogroupedtable.qza $ogroupedtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <param label="--p-axis: " name="paxis" optional="False" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <option value="feature">feature</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <option value="sample">sample</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 <param label="--p-mode: " name="pmode" optional="False" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 <option value="median-ceiling">median-ceiling</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <option value="mean-ceiling">mean-ceiling</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <option value="sum">sum</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
4
florianbegusch
parents: 0
diff changeset
35 <param label="--m-metadata-file [required]" name="mmedatafile" type="data" format="tabular,qza,no_unzip.zip" />
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 Group samples or features by a metadata column
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 ##############################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 Group samples or features in a feature table using metadata to define the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 mapping of IDs to a group.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 The table to group samples or features on.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 axis : Str % Choices('sample', 'feature')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 Along which axis to group. Each ID in the given axis must exist in
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 `metadata`.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 metadata : MetadataColumn[Categorical]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 A column defining the groups. Each unique value will become a new ID
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 for the table on the given `axis`.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 How to combine samples or features within a group. `sum` will sum the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 frequencies across all samples or features within a group; `mean-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 ceiling` will take the ceiling of the mean of these frequencies;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 `median-ceiling` will take the ceiling of the median of these
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 frequencies.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 grouped_table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 A table that has been grouped along the given `axis`. IDs on that axis
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 are replaced by values in the `metadata` column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 </tool>