|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-table_subsample" name="qiime feature-table subsample" version="2018.4">
|
|
|
3 <description> - Subsample table</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 <![CDATA[
|
|
|
9 qiime feature-table subsample --i-table=$itable --p-subsampling-depth="$psubsamplingdepth" --p-axis=$paxis
|
|
|
10
|
|
|
11 #if str($cmdconfig) != 'None':
|
|
|
12 --cmd-config=$cmdconfig
|
|
|
13 #end if
|
|
|
14 --o-sampled-table=osampledtable;
|
|
|
15
|
|
|
16 cp osampledtable.qza $osampledtable;
|
|
|
17 ]]>
|
|
|
18 </command>
|
|
|
19 <inputs>
|
|
|
20 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be sampled. [required]" name="itable" optional="False" type="data"/>
|
|
|
21
|
|
|
22 <param label="--p-subsampling-depth: The total number of samples or features to be randomly sampled. Samples or features that are reduced to a zero sum will not be included in the resulting table. [required]" name="psubsamplingdepth" optional="False" type="text"/>
|
|
|
23
|
|
|
24 <param label="--p-axis: The axis to sample over. If 'sample' then
|
|
|
25 samples will be randomly selected to be
|
|
|
26 retained. If 'feature' then a random set of
|
|
|
27 features will be selected to be retained.
|
|
|
28 [required]" name="paxis" optional="False" type="select">
|
|
|
29 <option value="sample">sample</option>
|
|
|
30 <option value="feature">feature</option>
|
|
|
31 </param>
|
|
|
32
|
|
|
33 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
34 </inputs>
|
|
|
35 <outputs>
|
|
|
36 <data format="qza" label="${tool.name} on ${on_string}: sampled-table.qza" name="osampledtable"/>
|
|
|
37 </outputs>
|
|
|
38 <help>
|
|
|
39 <![CDATA[
|
|
|
40 Subsample table
|
|
|
41 ----------------
|
|
|
42
|
|
|
43 Randomly pick samples or features, without replacement, from the table.
|
|
|
44
|
|
|
45 Parameters
|
|
|
46 ----------
|
|
|
47 table : FeatureTable[Frequency]
|
|
|
48 The feature table to be sampled.
|
|
|
49 subsampling_depth : Int % Range(1, None)
|
|
|
50 The total number of samples or features to be randomly sampled. Samples
|
|
|
51 or features that are reduced to a zero sum will not be included in the
|
|
|
52 resulting table.
|
|
|
53 axis : Str % Choices({'feature', 'sample'})
|
|
|
54 The axis to sample over. If "sample" then samples will be randomly
|
|
|
55 selected to be retained. If "feature" then a random set of features
|
|
|
56 will be selected to be retained.
|
|
|
57
|
|
|
58 Returns
|
|
|
59 -------
|
|
|
60 sampled_table : FeatureTable[Frequency]
|
|
|
61 The resulting subsampled feature table.
|
|
|
62 ]]>
|
|
|
63 </help>
|
|
|
64 </tool>
|
