comparison goseq.xml @ 11:602de62d995b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c

10:43798b4caee0

<tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>tests for overrepresented gene categories</description>
    <xrefs>
        <xref type="bio.tools">goseq</xref>
    </xrefs>
    <edam_topics>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_2436</edam_operation>
    </edam_operations>
    <macros>
        <token name="@TOOL_VERSION@">1.44.0</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-goseq</requirement>
        <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement>
        <requirement type="package" version="3.13.0">bioconductor-org.rn.eg.db</requirement>
        <requirement type="package" version="1.0.9">r-dplyr</requirement>
        <requirement type="package" version="3.3.6">r-ggplot2</requirement>
        <requirement type="package" version="1.7.1">r-optparse</requirement>
        <requirement type="package" version="1.1.1o">openssl</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

                <param name="rdata_out" value="false"/>
            </section>
            <output name="wallenius_tab">
                <assert_contents>
                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
                    <has_text_matching expression="GO:0005576.*0.9" />
                </assert_contents>
            </output>
            <output name="cat_genes_tab">
                <assert_contents>
                    <has_text_matching expression="category.*de_genes" />

                <param name="rdata_out" value="false"/>
            </section>
            <output name="wallenius_tab">
                <assert_contents>
                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
                    <has_text_matching expression="GO:0016569.*0.90" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure length bias plot works -->
        <test expect_num_outputs="2">

**Inputs**

*Differentially expressed genes file*

goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute an expression on every row" tool to create a True / False column for your dataset.

Example:

    =============== =====
    ENSG00000236824 False

11:602de62d995b

<tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>tests for overrepresented gene categories</description>
    <macros>
        <token name="@TOOL_VERSION@">1.50.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_2436</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">goseq</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-goseq</requirement>
        <requirement type="package" version="3.16.0">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.16.0">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="3.16.0">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="3.16.0">bioconductor-org.mm.eg.db</requirement>
        <requirement type="package" version="3.16.0">bioconductor-org.rn.eg.db</requirement>
        <requirement type="package" version="1.0.10">r-dplyr</requirement>
        <requirement type="package" version="3.4.0">r-ggplot2</requirement>
        <requirement type="package" version="1.7.3">r-optparse</requirement>
        <requirement type="package" version="1.1.1s">openssl</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

                <param name="rdata_out" value="false"/>
            </section>
            <output name="wallenius_tab">
                <assert_contents>
                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
                    <has_text_matching expression="GO:0012501.*0.01"/>
                </assert_contents>
            </output>
            <output name="cat_genes_tab">
                <assert_contents>
                    <has_text_matching expression="category.*de_genes" />

                <param name="rdata_out" value="false"/>
            </section>
            <output name="wallenius_tab">
                <assert_contents>
                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
                    <has_text_matching expression="GO:0015748.*0.02" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure length bias plot works -->
        <test expect_num_outputs="2">

**Inputs**

*Differentially expressed genes file*

goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute on rows" tool to create a True / False column for your dataset.

Example:

    =============== =====
    ENSG00000236824 False