comparison limma_voom.xml @ 26:119b069fc845 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738

25:d6f5fa4ee473

<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy0">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>
    <macros>
        <token name="@TOOL_VERSION@">3.50.1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">limma</xref>
    </xrefs>
    <edam_topics>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3563</edam_operation>
        <edam_operation>operation_3223</edam_operation>
    </edam_operations>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
        <requirement type="package" version="3.36.0">bioconductor-edger</requirement>
        <requirement type="package" version="1.4.36">r-statmod</requirement>
        <requirement type="package" version="1.1.1">r-scales</requirement>
        <requirement type="package" version="0.2.21">r-rjson</requirement>
        <requirement type="package" version="1.20.3">r-getopt</requirement>
        <requirement type="package" version="3.1.1">r-gplots</requirement>
        <requirement type="package" version="2.4.0">bioconductor-glimma</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: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

            <param name="cfile" value="yes" />
            <param name="cinfo" value="contrasts.txt" ftype="tabular" />
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="3">
                <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" />
                    </assert_contents>
                </element>
                <element name="limma-voom_WT-Mut" 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" />
                    </assert_contents>
                </element>
                <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
                     <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.9146" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>

26:119b069fc845

<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>
    <macros>
        <token name="@TOOL_VERSION@">3.58.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">23.0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3563</edam_operation>
        <edam_operation>operation_3223</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">limma</xref>
        <xref type="bioconductor">limma</xref>
    </xrefs>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
        <requirement type="package" version="4.0.2">bioconductor-edger</requirement>
        <requirement type="package" version="1.5.0">r-statmod</requirement>
        <requirement type="package" version="1.3.0">r-scales</requirement>
        <requirement type="package" version="0.2.21">r-rjson</requirement>
        <requirement type="package" version="1.20.4">r-getopt</requirement>
        <requirement type="package" version="3.1.3.1">r-gplots</requirement>
        <requirement type="package" version="2.12.0">bioconductor-glimma</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: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

            <param name="cfile" value="yes" />
            <param name="cinfo" value="contrasts.txt" ftype="tabular" />
            <param name="normalisationOption" value="TMM" />
            <param name="topgenes" value="6" />
            <output_collection name="outTables" count="3">
                <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
                     <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
                        <has_text_matching expression="11304.*0.9146" />
                    </assert_contents>
                </element>
                <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" />
                    </assert_contents>
                </element>
                <element name="limma-voom_WT-Mut" 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" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>