comparison scran_normalize.xml @ 2:6864acb21714 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c

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>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[ 
        Rscript $__tool_directory__/scran-normalize.R 
            --data '$input'
            --sep '$input_sep' 
            #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>
            <option value=",">Comma</option>
        </param>
        <conditional name="metacell">
            <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details">
                <option value="Yes">Yes</option>
                <option value="No" selected="true">No</option>
            </param>

        <data name="output" format="tabular" label="Normalized Log counts of ${on_string}">
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <output name="output" file="logcounts.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="cluster" value="Yes"/>
            <param name="method" value="igraph"/>
            <param name="size" value="25"/>
            <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tab" ftype="tabular"/>
            <param name="cluster" value="Yes"/>
            <param name="method" value="hclust"/>
            <param name="size" value="25"/>
            <output name="output" file="logcounts_hclust.tsv" ftype="tabular"/>
        </test>

2:6864acb21714

<tool id="scran_normalize" name="scran_normalize" version="1.28.1+galaxy0">
    <description>Normalize raw counts expression values using deconvolution size factors</description>
    <requirements>
        <requirement type="package" version="1.28.1">bioconductor-scran</requirement>
        <requirement type="package" version="1.63_1">r-dynamictreecut</requirement>
        <requirement type="package" version="1.7.3">r-optparse</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[ 
        Rscript $__tool_directory__/scran-normalize.R 
            --data '$input'
            #if $metacell.cluster == "Yes":
                --cluster
                --method '$metacell.method'
                --size '$metacell.size'
            #end if
            -o '${output}'
]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Raw counts of expression data" help = "A tsv file that must have an header line"/>
        <conditional name="metacell">
            <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details">
                <option value="Yes">Yes</option>
                <option value="No" selected="true">No</option>
            </param>

        <data name="output" format="tabular" label="Normalized Log counts of ${on_string}">
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="counts.tsv" ftype="tabular"/>
            <output name="output" file="logcounts.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tsv" ftype="tabular"/>
            <param name="cluster" value="Yes"/>
            <param name="method" value="igraph"/>
            <param name="size" value="25"/>
            <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="counts.tsv" ftype="tabular"/>
            <param name="cluster" value="Yes"/>
            <param name="method" value="hclust"/>
            <param name="size" value="25"/>
            <output name="output" file="logcounts_hclust.tsv" ftype="tabular"/>
        </test>