comparison macros.xml @ 7:96336c6a2bb7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135

6:84fd33a60b35

        <xrefs>
            <xref type="bio.tools">dada2</xref>
            <xref type="bioconductor">dada2</xref>
        </xrefs>
    </xml>
    <token name="@DADA2_VERSION@">1.20</token>
    <token name="@WRAPPER_VERSION@">1</token>

    <xml name="version_command">
        <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
        ]]></version_command>

         - 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>

        </conditional>
    </xml>

    <!-- 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."/>
            <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
        </section>
    </xml>
    <xml name="filters">
        <section name="filter" title="Filtering parameters">
            <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
            <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
            <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
            <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
            <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>

7:96336c6a2bb7

        <xrefs>
            <xref type="bio.tools">dada2</xref>
            <xref type="bioconductor">dada2</xref>
        </xrefs>
    </xml>
    <token name="@DADA2_VERSION@">1.28</token>
    <token name="@WRAPPER_VERSION@">0</token>

    <xml name="version_command">
        <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
        ]]></version_command>

         - 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 ) {
         x <- read.table(fname, header=F, sep="\t")
         n <-x[,2]
         names(n)<-x[,1]
         return(n)
    }
    #def read_data($dataset)
        #if $dataset.is_of_type('dada2_sequencetable')
            t(read.table('$dataset', header=T, sep="\t", row.names=1, check.names=FALSE))
        #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, check.names=FALSE)
        #else
            readRDS('$dataset')
        #end if
    #end def
    ]]></token>

        </conditional>
    </xml>

    <!-- for filterAndTrim -->
    <xml name="trimmers">
        <section name="trim" title="Trimming parameters" expanded="true">
            <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."/>
            <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
        </section>
    </xml>
    <xml name="filters">
        <section name="filter" title="Filtering parameters" expanded="true">
            <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
            <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
            <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
            <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
            <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>