comparison limma_voom.xml @ 7:5a722ae502b3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33

6:6c9be744c932

<tool id="limma_voom" name="limma" version="3.34.9.2">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>

        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="0.5.0">r-scales</requirement>
        <requirement type="package" version="0.2.15">r-rjson</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
    </requirements>

    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
#import json
Rscript '$__tool_directory__/limma_voom.R'

#end if

-l '$adv.lfc'
-p '$adv.pVal'
-d '$adv.pAdjust'
-v '$adv.volgenes'
#if $adv.treat:
    -T
#end if

#if $deMethod.de_select == 'voom':

                <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="volgenes" type="integer" value="10" min="0"
                label="Number of genes to highlight in Volcano plot"
                help="The top DE genes will be highlighted in the Volcano plot for each contrast. 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>

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4573" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*Abca4.*0.4573" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="RData" />
                </assert_contents>
            </output>

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1" >
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4590" />

            <param name="counts" value="matrix.txt" />
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4590" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4573" />

                <param name="contrast" value="Mut-WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="normCounts" value="true" />
            <output_collection name="outTables" count="3">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="de_select" value="trend" />
            <param name="rdaOption" value="true" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="The limma-trend method was used" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="de_select" value="trend" />
            <param name="rdaOption" value="true" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="The limma-trend method was used" />

7:5a722ae502b3

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

    <requirements>

        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="0.5.0">r-scales</requirement>
        <requirement type="package" version="0.2.15">r-rjson</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="3.0.1">r-gplots</requirement>
    </requirements>

    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
#import json
Rscript '$__tool_directory__/limma_voom.R'

#end if

-l '$adv.lfc'
-p '$adv.pVal'
-d '$adv.pAdjust'
-G '$adv.topgenes'
#if $adv.treat:
    -T
#end if

#if $deMethod.de_select == 'voom':

                <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>

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4573" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*Abca4.*0.4573" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="RData" />
                </assert_contents>
            </output>

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="1" >
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4590" />

            <param name="counts" value="matrix.txt" />
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4590" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.4573" />

                <param name="contrast" value="Mut-WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="topgenes" value="6" />
            <param name="normCounts" value="true" />
            <output_collection name="outTables" count="3">
                <element name="limma-voom_Mut-WT" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <param name="de_select" value="trend" />
            <param name="rdaOption" value="true" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="The limma-trend method was used" />

            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <param name="de_select" value="trend" />
            <param name="rdaOption" value="true" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="The limma-trend method was used" />