|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2018.2">
|
|
|
3 <description> - Add pseudocount to table</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8
|
|
|
9 qiime composition add-pseudocount --i-table=$itable
|
|
|
10
|
|
|
11 #if $ppseudocount:
|
|
|
12 --p-pseudocount=$ppseudocount
|
|
|
13 #end if
|
|
|
14
|
|
|
15 #if str($cmdconfig) != 'None':
|
|
|
16 --cmd-config=$cmdconfig
|
|
|
17 #end if
|
|
|
18
|
|
|
19 --o-composition-table=ocompositiontable
|
|
|
20 ;
|
|
|
21 cp ocompositiontable.qza $ocompositiontable
|
|
|
22
|
|
|
23 ]]></command>
|
|
|
24 <inputs>
|
|
|
25 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] - The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data"/>
|
|
|
26 <param label="--p-pseudocount: The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/>
|
|
|
27 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
28 </inputs>
|
|
|
29 <outputs>
|
|
|
30 <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable"/>
|
|
|
31 </outputs>
|
|
|
32 <help><![CDATA[
|
|
|
33 Add pseudocount to table
|
|
|
34 ------------------------
|
|
|
35
|
|
|
36 Increment all counts in table by pseudocount.
|
|
|
37
|
|
|
38 Parameters
|
|
|
39 ----------
|
|
|
40 table : FeatureTable[Frequency]
|
|
|
41 The feature table to which pseudocounts should be added.
|
|
|
42 pseudocount : Int, optional
|
|
|
43 The value to add to all counts in the feature table.
|
|
|
44
|
|
|
45 Returns
|
|
|
46 -------
|
|
|
47 composition_table : FeatureTable[Composition]
|
|
|
48 The resulting feature table.
|
|
|
49 ]]>
|
|
|
50 </help>
|
|
|
51 </tool>
|
