comparison limma_voom.xml @ 12:81796eb60bd0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c

11:7e8af58c8052

<tool id="limma_voom" name="limma" version="3.34.9.7">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>

    #end if
#end if

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

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

                <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="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"

                        <has_text_matching expression="11304.*0.4590" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Ensure normalised counts file output works-->
        <test>
            <param name="format" value="matrix" />
            <param name="normCounts" value="true" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </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" />
                    </assert_contents>
                </element>
                <element name="limma-voom_normcounts" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
                        <has_text_matching expression="11304.*15.7545" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Ensure multiple counts files input works -->

12:81796eb60bd0

<tool id="limma_voom" name="limma" version="3.34.9.8">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>

    #end if
#end if

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

#if $out.filtCounts:
    -F
#end if

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

                <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="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                label="Output Filtered Counts Table?"
                help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No">
            </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="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"

                        <has_text_matching expression="11304.*0.4590" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Ensure filtered and normalised count outputs works-->
        <test>
            <param name="format" value="matrix" />
            <param name="filtCounts" value="true" />
            <param name="normCounts" value="true" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="filt_select" value="yes" />
            <param name="format_select" value="counts"/>
            <param name="cntReq" value="10"/>
            <param name="count_select" value="sample"/>
            <param name="cntSampleReq" value="3"/>
            <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.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" />
                    </assert_contents>
                </element>
                <element name="limma-voom_normcounts" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
                        <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" />
                    </assert_contents>
                </element>
                <element name="limma-voom_filtcounts" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
                        <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" />
                        <not_has_text text="11302"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Ensure multiple counts files input works -->