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comparison qiime2/qiime_feature-table_subsample.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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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 <macros>
65 <import>qiime_citation.xml</import>
66 </macros>
67 <expand macro="qiime_citation" />
68 </tool>