comparison limma_voom.xml @ 8:00a42b66e522 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623

7:e6a4ff41af6b

<tool id="limma_voom" name="limma" version="3.34.9.3">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>

            -y
        #elif $f.filt.cformat.samples.count_select == 'sample':
            -s '$f.filt.cformat.samples.cntSampleReq'
        #end if
    #end if
#end if

#if $out.normCounts:
    -x
#end if

            <when value="no" />
        </conditional>

        <!-- Contrasts -->
        <repeat name="rep_contrast" title="Contrast" min="1" default="1">
            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
                <validator type="empty_field" />
                <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
            </param>
        </repeat>

        <!-- Filter Options -->
        <section name="f" expanded="false" title="Filter Low Counts">

            </conditional>
        </section>

        <!-- Output Options -->
        <section name="out" expanded="false" title="Output Options">
            <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                label="Output Normalised Counts Table?"
                help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
            </param>
            <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>

                <option value="none">None</option>
            </param>
            <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
                label="Test significance relative to a fold-change threshold (TREAT)"
                help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
            <param name="topgenes" type="integer" value="10" min="0"
                label="Number of genes to highlight in Volcano plot and Heatmap"
                help="The top DE genes will be highlighted in the Volcano plot for each contrast and output in a heatmap PDF. Default: 10."/>
            <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
                <option value="TMM" selected="true">TMM</option>
                <option value="RLE">RLE</option>
                <option value="upperquartile">Upperquartile</option>
                <option value="none">None (Don't normalise)</option>

8:00a42b66e522

<tool id="limma_voom" name="limma" version="3.34.9.4">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>

            -y
        #elif $f.filt.cformat.samples.count_select == 'sample':
            -s '$f.filt.cformat.samples.cntSampleReq'
        #end if
    #end if
#end if

#if $out.plots:
    -P $out.plots
#end if

#if $out.normCounts:
    -x
#end if

            <when value="no" />
        </conditional>

        <!-- Contrasts -->
        <repeat name="rep_contrast" title="Contrast" min="1" default="1">
            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
                <validator type="empty_field" />
                <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
            </param>
        </repeat>

        <!-- Filter Options -->
        <section name="f" expanded="false" title="Filter Low Counts">

            </conditional>
        </section>

        <!-- Output Options -->
        <section name="out" expanded="false" title="Output Options">
            <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs">
                <option value="d">Density Plots (if filtering)</option>
                <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
                <option value="b">Box Plots (if normalising)</option>
                <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
                <option value="m">MD Plots for individual samples</option>
                <option value="h">Heatmaps (top DE genes) </option>
                <option value="s">Stripcharts (top DE genes)</option>
            </param>
            <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                label="Output Normalised Counts Table?"
                help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
            </param>
            <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>

                <option value="none">None</option>
            </param>
            <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
                label="Test significance relative to a fold-change threshold (TREAT)"
                help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
            <param name="topgenes" type="integer" value="10" min="0" max="100"
                label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
                help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/>
            <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
                <option value="TMM" selected="true">TMM</option>
                <option value="RLE">RLE</option>
                <option value="upperquartile">Upperquartile</option>
                <option value="none">None (Don't normalise)</option>