Mercurial > repos > florianbegusch > qiime2
changeset 4:19706b0f5de7 draft
Uploaded
author | florianbegusch |
---|---|
date | Wed, 23 May 2018 10:52:14 -0400 |
parents | 1722a584c78c |
children | 4d6f4d340a9e |
files | qiime_composition_add-pseudocount.xml |
diffstat | 1 files changed, 51 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime_composition_add-pseudocount.xml Wed May 23 10:52:14 2018 -0400 @@ -0,0 +1,51 @@ +<?xml version="1.0" ?> +<tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2018.2"> + <description> - Add pseudocount to table</description> + <requirements> + <requirement type="package" version="2018.4">qiime2</requirement> + </requirements> + <command><![CDATA[ + + qiime composition add-pseudocount --i-table=$itable + + #if $ppseudocount: + --p-pseudocount=$ppseudocount + #end if + + #if str($cmdconfig) != 'None': + --cmd-config=$cmdconfig + #end if + + --o-composition-table=ocompositiontable + ; + cp ocompositiontable.qza $ocompositiontable + +]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] - The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data"/> + <param label="--p-pseudocount: The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/> + <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> + </inputs> + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable"/> + </outputs> + <help><![CDATA[ +Add pseudocount to table +------------------------ + +Increment all counts in table by pseudocount. + +Parameters +---------- +table : FeatureTable[Frequency] + The feature table to which pseudocounts should be added. +pseudocount : Int, optional + The value to add to all counts in the feature table. + +Returns +------- +composition_table : FeatureTable[Composition] + The resulting feature table. + ]]> +</help> +</tool>