comparison deseq2.xml @ 46:151ed7b41985 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c

45:702bdf59d6c8

                    <has_text_matching expression="FBgn0003360\t1933\.950.*\t-2\.88.*\t0\.111.*\t-25\.8.*\t.*e-14[0-9]\t.*e-14[0-9]"/>
                    <has_n_lines n="3999"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

46:151ed7b41985

                    <has_text_matching expression="FBgn0003360\t1933\.950.*\t-2\.88.*\t0\.111.*\t-25\.8.*\t.*e-14[0-9]\t.*e-14[0-9]"/>
                    <has_n_lines n="3999"/>
                </assert_contents>
            </output>
        </test>
        <!--Test sample_sheet_contrasts with numeric factor column in design formula -->
        <test expect_num_outputs="2">
            <param name="select_data|how" value="sample_sheet_contrasts"/>
            <param name="select_data|countsFile">
                <collection type="list">
                    <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
                    <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
                    <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
                    <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
                    <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
                    <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
                    <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
                </collection>
            </param>
            <param name="select_data|sample_sheet" value="sample_sheet_numeric.tab"/>
            <param name="select_data|design_formula_mode|mode" value="custom"/>
            <param name="select_data|design_formula_mode|design_formula" value="~ replicate + treatment"/>
            <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
            <section name="advanced_options">
                <param name="use_beta_priors" value="1"/>
            </section>
            <section name="output_options">
                <param name="output_selector" value="normCounts"/>
            </section>
            <output name="counts_out">
                <assert_contents>
                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
                    <has_n_columns n="8"/>
                </assert_contents>
            </output>
            <output name="deseq_out">
                <assert_contents>
                    <!-- Multi-factor design with numeric replicate column -->
                    <has_text_matching expression="FBgn0003360\t1933\.950.*"/>
                    <has_n_lines n="3999"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**