comparison goseq.xml @ 9:ef2ad746b589 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"

8:8b3e3657034e

<tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@">
    <description>tests for overrepresented gene categories</description>
    <macros>
        <token name="@VERSION@">1.36.0</token>
        <token name="@GALAXY_VERSION@">galaxy0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement>
        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
        <requirement type="package" version="0.8.3">r-dplyr</requirement>
        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
        <requirement type="package" version="1.6.2">r-optparse</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

                <param name="rdata_out" value="false"/>
            </section>
            <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/>
            <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:0000278.*0.01" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure getting GO categories works & also DE genes for GO terms-->

                <param name="cat_genes" value="true"/>
                <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.*9.0" />
                </assert_contents>
            </output>
            <output name="cat_genes_tab">
                <assert_contents>
                    <has_text_matching expression="Categories.*DEgenes" />
                    <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure getting GO categories for another genome (zebrafish) works -->

                <param name="cat_genes" value="false"/>
                <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.*0.8" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure length bias plot works -->
        <test expect_num_outputs="2">

This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced.

Example:

=========== =============== ================ ============ ========== ======================================== ========== =================== ====================
*category*  *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term*                                   *ontology* *p.adjust.over_rep* *p.adjust.under_rep*
----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- --------------------
GO\:0005576  0.000054        0.999975         56           142       extracellular region                     CC         0.394825             1
GO\:0005840  0.000143        0.999988         9            12        ribosome                                 CC         0.394825             1
GO\:0044763  0.000252        0.999858         148          473       single-organism cellular process         BP         0.394825             1
GO\:0044699  0.000279        0.999844         158          513       single-organism process                  BP         0.394825             1

9:ef2ad746b589

<tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@">
    <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="@VERSION@">1.44.0</token>
        <token name="@GALAXY_VERSION@">galaxy0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@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="1.0.6">r-dplyr</requirement>
        <requirement type="package" version="3.3.3">r-ggplot2</requirement>
        <requirement type="package" version="1.6.6">r-optparse</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

                <param name="rdata_out" value="false"/>
            </section>
            <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/>
            <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:0000278.*0.01" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure getting GO categories works & also DE genes for GO terms-->

                <param name="cat_genes" value="true"/>
                <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" />
                    <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure getting GO categories for another genome (zebrafish) works -->

                <param name="cat_genes" value="false"/>
                <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">

This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced.

Example:

=========== =============== ================ ============ ========== ======================================== ========== =================== ====================
*category*  *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term*                                   *ontology* *p_adjust_over_rep* *p_adjust_under_rep*
----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- --------------------
GO\:0005576  0.000054        0.999975         56           142       extracellular region                     CC         0.394825             1
GO\:0005840  0.000143        0.999988         9            12        ribosome                                 CC         0.394825             1
GO\:0044763  0.000252        0.999858         148          473       single-organism cellular process         BP         0.394825             1
GO\:0044699  0.000279        0.999844         158          513       single-organism process                  BP         0.394825             1