comparison edger.xml @ 7:334ce9b1bac5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36

6:555659de7321

<tool id="edger" name="edgeR" version="3.24.1">
    <description>
        Perform differential expression of count data
    </description>

    <requirements>

            <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">

                    <not_has_text text="likelihood ratio" />
                    <not_has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure annotation file input works -->
        <test>
            <param name="format" value="matrix" />
            <param name="annoOpt" value="yes" />
            <param name="geneanno" value="anno.txt" />

7:334ce9b1bac5

<tool id="edger" name="edgeR" version="3.24.1+galaxy1">
    <description>
        Perform differential expression of count data
    </description>

    <requirements>

            <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. (MT.t1-MT.t0)-(WT.t1-WT.t0). 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 or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons.">
                <validator type="empty_field" />
                <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
            </param>
        </repeat>

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

                    <not_has_text text="likelihood ratio" />
                    <not_has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <!-- Complex contrasts constructions -->
        <test>
            <param name="format" value="matrix" />
            <param name="counts" value="matrix-complex.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="(MutA-MutB)-(WTA-WTB)" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1">
                <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular" >
                    <assert_contents>
                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
                        <has_text_matching expression="11304.*15.53" />
                   </assert_contents>
               </element>
            </output_collection>
            <output name="outReport" >
                <assert_contents>
                    <has_text text="edgeR Analysis Output" />
                    <has_text text="quasi-likelihood" />
                    <not_has_text text="likelihood ratio" />
                    <not_has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure annotation file input works -->
        <test>
            <param name="format" value="matrix" />
            <param name="annoOpt" value="yes" />
            <param name="geneanno" value="anno.txt" />