Mercurial > repos > iuc > dada2_removebimeradenovo

comparison dada2_removeBimeraDenovo.xml @ 7:7136e9ab70db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135
author iuc
date Mon, 07 Aug 2023 01:33:57 +0000
parents 1bc3657cd694
children
comparison
equal deleted inserted replaced
6:1bc3657cd694 7:7136e9ab70db
31 write.data( seqtab.nochim, '$stable_sequencetable', "dada2_sequencetable" ) 31 write.data( seqtab.nochim, '$stable_sequencetable', "dada2_sequencetable" )
32 #else if $unqs.is_of_type('dada2_mergepairs') 32 #else if $unqs.is_of_type('dada2_mergepairs')
33 write.data( seqtab.nochim, '$stable_mergepairs', "dada2_mergepairs" ) 33 write.data( seqtab.nochim, '$stable_mergepairs', "dada2_mergepairs" )
34 #end if 34 #end if
35 35
36 ## dada input 36 cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%")
37 if(class(unqs)=="list"){
38 unqssum<-lapply(lapply(unqs, getUniques),sum)
39 outsum<-lapply(seqtab.nochim,sum)
40 mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum)
41 cat("remaining nonchimeric: ", mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum), "%")
42 }else{
43 cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%")
44 }
45 ]]></configfile> 37 ]]></configfile>
46 </configfiles> 38 </configfiles>
47 <inputs> 39 <inputs>
48 <param name="unqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable" label="sequence table" help=""/> 40 <param name="unqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable" label="sequence table" help=""/>
49 <param argument="method" type="select" label="Method"> 41 <param argument="method" type="select" label="Method">