comparison deseq2.xml @ 24:71bacea10eee draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"

23:0696db066a5b

<tool id="deseq2" name="DESeq2" version="2.11.40.6">
    <description>Determines differentially expressed features from count tables</description>
    <macros>
        <import>deseq2_macros.xml</import>
    </macros>
    <requirements>

                <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
            </actions>
        </data>
        <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
            <filter>many_contrasts is True</filter>
            <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
        </collection>
        <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
            <filter>pdf == True</filter>
        </data>
        <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">

                <assert_contents>
                    <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

24:71bacea10eee

<tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
    <description>Determines differentially expressed features from count tables</description>
    <macros>
        <import>deseq2_macros.xml</import>
    </macros>
    <requirements>

                <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
            </actions>
        </data>
        <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
            <filter>many_contrasts is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
        </collection>
        <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
            <filter>pdf == True</filter>
        </data>
        <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">

                <assert_contents>
                    <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
                </assert_contents>
            </output>
        </test>
        <!--Ensure many_contrasts produces output collection -->
        <test expect_num_outputs="1">
            <param name="select_data|how" value="group_tags"/>
            <param name="select_data|countsFile">
                <collection type="list">
                    <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
                    <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
                    <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
                    <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
                    <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
                    <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
                </collection>
            </param>
            <repeat name="rep_factorName">
                <param name="factorName" value="Treatment"/>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" value="Treated"/>
                    <param name="groups" value="primary:treated"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" value="Untreated"/>
                    <param name="groups" value="primary:untreated"/>
                </repeat>
            </repeat>
            <param name="pdf" value="False"/>
            <param name="tximport_selector" value="tximport"/>
            <param name="txtype" value="sailfish"/>
            <param name="mapping_format_selector" value="tabular"/>
            <param name="tabular_file" value="tx2gene.tab"/>
            <param name="many_contrasts" value="true"/>
            <output_collection name="split_output" type="list" count="1">
                <element name="Treatment_Treated_vs_Untreated">
                    <assert_contents>
                        <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**