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comparison qiime2/qiime_feature-table_group.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 914fa4daf16a
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.4">
3 <description> - Group samples or features by a metadata column</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
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
16 #if $input_files_mmetadatafile:
17 #def list_dict_to_string(list_dict):
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
19 #for d in list_dict[1:]:
20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
21 #end for
22 #return $file_list
23 #end def
24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
25 #end if
26
27
28 --o-grouped-table=ogroupedtable
29 ;
30 cp ogroupedtable.qza $ogroupedtable
31 ]]></command>
32 <inputs>
33 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data"/>
34 <param label="--p-axis: " name="paxis" optional="False" type="select">
35 <option value="feature">feature</option>
36 <option value="sample">sample</option>
37 </param>
38 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] A column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text"/>
39 <param label="--p-mode: " name="pmode" optional="False" type="select">
40 <option value="median-ceiling">median-ceiling</option>
41 <option value="mean-ceiling">mean-ceiling</option>
42 <option value="sum">sum</option>
43 </param>
44
45 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
46 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
47 </repeat>
48
49 </inputs>
50 <outputs>
51 <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable"/>
52 </outputs>
53 <help><![CDATA[
54 Group samples or features by a metadata column
55 ##############################################
56
57 Group samples or features in a feature table using metadata to define the
58 mapping of IDs to a group.
59
60 Parameters
61 ----------
62 table : FeatureTable[Frequency]
63 The table to group samples or features on.
64 axis : Str % Choices('sample', 'feature')
65 Along which axis to group. Each ID in the given axis must exist in
66 `metadata`.
67 metadata : MetadataColumn[Categorical]
68 A column defining the groups. Each unique value will become a new ID
69 for the table on the given `axis`.
70 mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
71 How to combine samples or features within a group. `sum` will sum the
72 frequencies across all samples or features within a group; `mean-
73 ceiling` will take the ceiling of the mean of these frequencies;
74 `median-ceiling` will take the ceiling of the median of these
75 frequencies.
76
77 Returns
78 -------
79 grouped_table : FeatureTable[Frequency]
80 A table that has been grouped along the given `axis`. IDs on that axis
81 are replaced by values in the `metadata` column.
82 ]]></help>
83 <macros>
84 <import>qiime_citation.xml</import>
85 </macros>
86 <expand macro="qiime_citation"/>
87 </tool>