view dada2_derepFastq.xml @ 0:3f0bbe41052f draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty

<tool id="dada2_derepFastq" name="dada2: derepFastq" version="@DADA2_VERSION@">
    <description>dereplicate amplicon sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
	mkdir '$derep.extra_files_path' &&
    Rscript '$dada2_script'
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
library(dada2, quietly=T)
derep <- derepFastq('$reads')

write.table(derep\$uniques, file = '$derep', quote = F, sep = "\t", row.names = T, col.names = F)
saveRDS(derep, file=file.path('$derep.extra_files_path', "Rdata"))
    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data" />
    </inputs>
    <outputs>
        <data name="derep" format="dada2_derep" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="reads" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
            <output name="output" value="derepFastq_single_F3D0_R1.table" ftype="dada2_derep" />
        </test>
    </tests>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
    <expand macro="citations"/>
</tool>