comparison macros.xml @ 9:ef3ebaa70032 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c

8:af8d1ccbd153

    </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")

            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(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."/>
            <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"/>

9:ef3ebaa70032

    </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")

            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(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
    }else{
        saveRDS(data, file=fname)
    }
}
    ]]></token>

    <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
        <conditional name="paired_cond">
            <param name="paired_select" type="select" label="Paired reads">
                <option value="paired">paired - in a data set pair</option>
                <option value="separate">paired - in two separate data sets</option>
                <option value="single">single</option>
            </param>
            <when value="paired">
                <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
            </when>
            <when value="separate">
                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
            </when>
            <when value="single">
                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
            </when>
        </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"/>