comparison macros.xml @ 5:9aeea74a1fc9 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

4:9f888de151d1

        </citations>
    </xml>

    <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>

    <token name="@READ_FOO@"><![CDATA[
    #def read_data($dataset)
        #if $dataset.is_of_type('dada2_derep')
            readRDS('$dataset)
        #else if $dataset.is_of_type('dada2_dada')
            readRDS('$dataset')
        #else if $dataset.is_of_type('dada2_sequencetable')
            as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )
        #else if $dataset.is_of_type('dada2_mergepairs')
              readRDS('$dataset')
        #else if $dataset.is_of_type('tabular')
              read.table('$dataset', header=T, sep="\t", row.names=1 )
        #else
            #raise Exception("error: unknown input type")
        #end if
    #end def
    ]]></token>
    <!-- for filterAndTrim -->
    <xml name="trimmers">
        <section name="trim" title="Trimming parameters">
            <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
            <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>

        </section>
    </xml>

    <xml name="errorEstimationFunction">
        <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
            <option value="loessErrfun">loess</option>
            <option value="noqualErrfun">noqual</option>
            <option value="PacBioErrfun">PacBio</option>
        </param>
    </xml>
    <token name="@HELP_OVERVIEW@"><![CDATA[
Overview
........

5:9aeea74a1fc9

        </citations>
    </xml>

    <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>

    <!-- function to read dada2 data types
         - derep, dada, and mergepairs are simply read as RDS 
         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
         - uniques is a named integer vector (columns=ASVs, only one rows)-->
    <token name="@READ_FOO@"><![CDATA[
    read.uniques <- function ( fname ) {
         p <- read.table(fname, header=F, sep="\t")
         n <-x[,2]
         names(n)<-x[,1]
    }
    #def read_data($dataset)
        #if $dataset.is_of_type('dada2_sequencetable')
            t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
        #else if $dataset.is_of_type('dada2_uniques')
            read.uniques('$dataset')
        #else if $dataset.is_of_type('tabular')
            read.table('$dataset', header=T, sep="\t", row.names=1)
        #else
            readRDS('$dataset')
        #end if
    #end def
    ]]></token>
    <!-- function to write dada2 data types (the content or the R variable 'out' is written)
         - derep, dada, and mergepairs are written as RDS 
         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
         - uniques is a named integer vector (columns=ASVs, only one rows)-->
    <token name="@WRITE_FOO@"><![CDATA[
write.data <- function( data, fname, type ){
    if( type == 'dada2_uniques'){
        write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F)
    }else if( type== 'dada2_sequencetable'){
        write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
    }else{
        saveRDS(data, file=fname)
    }
}
    ]]></token> 

    <!-- for filterAndTrim -->
    <xml name="trimmers">
        <section name="trim" title="Trimming parameters">
            <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
            <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>

        </section>
    </xml>

    <xml name="errorEstimationFunction">
        <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
            <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
            <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
            <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option>
        </param>
    </xml>
    <token name="@HELP_OVERVIEW@"><![CDATA[
Overview
........