view scater-read-10x-results.xml @ 0:da3f394039b5 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<tool id="scater_read_10x_results" name="Scater read 10x data" version="@TOOL_VERSION@+galaxy0">
    <description>Loads 10x data into a serialized scater R object</description>
    <macros>
        <import>scater_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$matrix' matrix.mtx;
        ln -s '$genes' genes.tsv;
        ln -s '$barcodes' barcodes.tsv;

        scater-read-10x-results.R -d ./ -o '$R_scater_serialized'
    ]]></command>
    <inputs>
        <param type="data" name="matrix" format="txt" help="File containing the matrix.mtx, genes.txt, barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name."/>
        <param type="data" name="genes" format="tsv" help="File containing the genes.txt, barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name."/>
        <param type="data" name="barcodes" format="tsv" help="File containing the barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name"/>
    </inputs>
    <outputs>
        <data name="R_scater_serialized" format="rdata" label=""/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="matrix.mtx"/>
            <param name="genes" value="genes.tsv"/>
            <param name="barcodes" value="barcodes.tsv"/>
            <output name="R_scater_serialized" file="R_scater_serialized.rds"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP@

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