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comparison qiime2/qiime_composition_add-pseudocount.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2019.7"> 2 <tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount"
3 <description> - Add pseudocount to table</description> 3 version="2020.8">
4 <requirements> 4 <description>Add pseudocount to table</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime composition add-pseudocount 9 qiime composition add-pseudocount
9 10
10 --i-table=$itable 11 --i-table=$itable
12
13 --p-pseudocount=$ppseudocount
14
11 --o-composition-table=ocompositiontable 15 --o-composition-table=ocompositiontable
12 16
13 #if str($ppseudocount): 17 #if str($examples) != 'None':
14 --p-pseudocount=$ppseudocount 18 --examples=$examples
15 #end if 19 #end if
20
16 ; 21 ;
17 cp ocompositiontable.qza $ocompositiontable 22 cp ocompositiontable.qza $ocompositiontable
18 ]]></command> 23
19 <inputs> 24 ]]></command>
20 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data"/> 25 <inputs>
21 <param label="--p-pseudocount: INTEGER The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/> 26 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data" />
22 </inputs> 27 <param label="--p-pseudocount: INTEGER The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1" />
23 <outputs> 28 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
24 <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable"/> 29
25 </outputs> 30 </inputs>
26 <help><![CDATA[ 31
32 <outputs>
33 <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable" />
34
35 </outputs>
36
37 <help><![CDATA[
27 Add pseudocount to table 38 Add pseudocount to table
28 ######################## 39 ###############################################################
29 40
30 Increment all counts in table by pseudocount. 41 Increment all counts in table by pseudocount.
31 42
32 Parameters 43 Parameters
33 ---------- 44 ----------
38 49
39 Returns 50 Returns
40 ------- 51 -------
41 composition_table : FeatureTable[Composition] 52 composition_table : FeatureTable[Composition]
42 The resulting feature table. 53 The resulting feature table.
43 ]]></help> 54 ]]></help>
44 <macros> 55 <macros>
45 <import>qiime_citation.xml</import> 56 <import>qiime_citation.xml</import>
46 </macros> 57 </macros>
47 <expand macro="qiime_citation"/> 58 <expand macro="qiime_citation"/>
48 </tool> 59 </tool>