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comparison qiime2-2020.8/qiime_composition_add-pseudocount.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount"
3 version="2020.8">
4 <description>Add pseudocount to table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime composition add-pseudocount
10
11 --i-table=$itable
12
13 --p-pseudocount=$ppseudocount
14
15 --o-composition-table=ocompositiontable
16
17 #if str($examples) != 'None':
18 --examples=$examples
19 #end if
20
21 ;
22 cp ocompositiontable.qza $ocompositiontable
23
24 ]]></command>
25 <inputs>
26 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data" />
27 <param label="--p-pseudocount: INTEGER The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1" />
28 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
29
30 </inputs>
31
32 <outputs>
33 <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable" />
34
35 </outputs>
36
37 <help><![CDATA[
38 Add pseudocount to table
39 ###############################################################
40
41 Increment all counts in table by pseudocount.
42
43 Parameters
44 ----------
45 table : FeatureTable[Frequency]
46 The feature table to which pseudocounts should be added.
47 pseudocount : Int, optional
48 The value to add to all counts in the feature table.
49
50 Returns
51 -------
52 composition_table : FeatureTable[Composition]
53 The resulting feature table.
54 ]]></help>
55 <macros>
56 <import>qiime_citation.xml</import>
57 </macros>
58 <expand macro="qiime_citation"/>
59 </tool>