view dada2_mergePairs.xml @ 3:caae353b2928 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty

<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
    <description>Merge denoised forward and reverse reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
    Rscript '$dada2_script'
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
library(dada2, quietly=T)

dadaF <- readRDS('$dadaf')
dadaR <- readRDS('$dadar')
derepF <- readRDS('$derepf')
derepR <- readRDS('$derepr')

merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minOverlap, maxMismatch = $maxMismatch,
    returnRejects = FALSE, propagateCol = character(0),
    justConcatenate = $justConcatenate, trimOverhang = $trimOverhang)

saveRDS(merged, file='$merged')
##For display in Galaxy this could be transposed (..but the user could also do it herself)
##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="dadaf" type="data" format="dada2_dada" label="Dada results for forward reads"/>
        <param name="derepf" type="data" format="dada2_derep" label="Dereplicated forward reads"/>
        <param name="dadar" type="data" format="dada2_dada" label="Dada results for reverse reads"/>
        <param name="derepr" type="data" format="dada2_derep" label="Dereplicated reverse reads"/>
        <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/>
        <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
        <param argument="justConcatenate" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
        <param argument="trimOverhang" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/>
    </inputs>
    <outputs>
        <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="dadaf" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
            <param name="derepf" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/>
            <param name="dadar" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
            <param name="derepr" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/>
            <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" />
        </test>
    </tests>
    <help><![CDATA[
Description
...........

This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap (at least 12bp by sefault) or which contain too many (>0 by default) mismatches in the overlap region.

Usage
.....

**Input**

- dereplicated reads and learned error rates of the forward reads
- dereplicated reads and learned error rates of the reversereads

**Output**

- a data set of type dada2_mergepairs (which is a RData file containing the output of dada2's mergePairs function).

Details
.......

@HELP_OVERVIEW@


    ]]></help>
    <expand macro="citations"/>
</tool>