comparison scran_normalize.xml @ 1:fb2f1b8b0013 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit e0357f07fdabee1ec6614aca6f7b51095111e0d5

0:252eded61848

<tool id="scran_normalize" name="scran_normalize" version="0.2.0">
    <description>Normalize raw counts expression values using deconvolution size factors</description>
    <requirements>
        <requirement type="package" version="1.6.2">r-optparse</requirement>
        <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement>
    </requirements>

            #if $metacell.cluster == "Yes":
                --cluster
                --method '$metacell.method'
                --size '$metacell.size'
            #end if
            -o ${output}
]]></command>
    <inputs>
        <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/>
        <param name="input_sep" type="select" label="Input column separator">
            <option value="tab" selected="true">Tabulation</option>

Note: First header row must NOT start with a '#' comment character

    </help>
    <citations>
        <citation type="bibtex">
            @Article{,
                author = {Aaron T. L. Lun and Davis J. McCarthy and John C. Marioni},
                title = {A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor},
                journal = {F1000Res.},
                year = {2016},
                volume = {5},
                pages = {2122},
                doi = {10.12688/f1000research.9501.2},
            }
        </citation>
    </citations>
</tool>

1:fb2f1b8b0013

<tool id="scran_normalize" name="scran_normalize" version="0.2.1">
    <description>Normalize raw counts expression values using deconvolution size factors</description>
    <requirements>
        <requirement type="package" version="1.6.2">r-optparse</requirement>
        <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement>
    </requirements>

            #if $metacell.cluster == "Yes":
                --cluster
                --method '$metacell.method'
                --size '$metacell.size'
            #end if
            -o '${output}'
]]></command>
    <inputs>
        <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/>
        <param name="input_sep" type="select" label="Input column separator">
            <option value="tab" selected="true">Tabulation</option>

Note: First header row must NOT start with a '#' comment character

    </help>
    <citations>
        <citation type="doi">10.12688/f1000research.9501.2</citation>
    </citations>
</tool>