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comparison qiime2/qiime_feature-table_rarefy.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_rarefy" name="qiime feature-table rarefy"
3 version="2020.8">
4 <description>Rarefy table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table rarefy
10
11 --i-table=$itable
12
13 --p-sampling-depth=$psamplingdepth
14
15 #if $pwithreplacement:
16 --p-with-replacement
17 #end if
18
19 --o-rarefied-table=orarefiedtable
20
21 #if str($examples) != 'None':
22 --examples=$examples
23 #end if
24
25 ;
26 cp orarefiedtable.qza $orarefiedtable
27
28 ]]></command>
29 <inputs>
30 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be rarefied. [required]" name="itable" optional="False" type="data" />
31 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to. Samples where the sum of frequencies is less than the sampling depth will be not be included in the resulting table unless subsampling is performed with replacement. [required]" name="psamplingdepth" optional="False" type="text" />
32 <param label="--p-with-replacement: --p-with-replacement: / --p-no-with-replacement Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]" name="pwithreplacement" selected="False" type="boolean" />
33 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
34
35 </inputs>
36
37 <outputs>
38 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
39
40 </outputs>
41
42 <help><![CDATA[
43 Rarefy table
44 ###############################################################
45
46 Subsample frequencies from all samples so that the sum of frequencies in
47 each sample is equal to sampling-depth.
48
49 Parameters
50 ----------
51 table : FeatureTable[Frequency]
52 The feature table to be rarefied.
53 sampling_depth : Int % Range(1, None)
54 The total frequency that each sample should be rarefied to. Samples
55 where the sum of frequencies is less than the sampling depth will be
56 not be included in the resulting table unless subsampling is performed
57 with replacement.
58 with_replacement : Bool, optional
59 Rarefy with replacement by sampling from the multinomial distribution
60 instead of rarefying without replacement.
61
62 Returns
63 -------
64 rarefied_table : FeatureTable[Frequency]
65 The resulting rarefied feature table.
66 ]]></help>
67 <macros>
68 <import>qiime_citation.xml</import>
69 </macros>
70 <expand macro="qiime_citation"/>
71 </tool>