comparison annotateMyIDs.xml @ 13:133f36c29579 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8

12:fe3ca740a485

    <description>annotate a generic set of identifiers</description>
    <xrefs>
        <xref type="bio.tools">annotatemyids</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">3.14.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>

        <test expect_num_outputs="1">
            <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
            <param name="id_type" value="ENSEMBL"/>
            <param name="organism" value="Hs"/>
            <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
            <output name="out_tab" file="out_gokegg.tab" />
        </test>
        <!-- Ensure duplicate Gene ID removal works -->
        <test expect_num_outputs="1">
            <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
            <param name="id_type" value="ENSEMBL"/>
            <param name="organism" value="Hs"/>
            <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
            <param name="remove_dups" value="True" />
            <output name="out_tab" file="out_gokegg_dupsrem.tab" />
        </test>
        <!-- Arabidopsis database -->
        <test expect_num_outputs="1">
            <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/>
            <param name="id_type" value="SYMBOL"/>
            <param name="organism" value="At"/>
            <param name="output_cols" value="GO,ENTREZID" />
            <output name="out_tab" file="out_arabidopsis.tab" />
        </test>
        <!-- Gallus gallus database -->
        <test expect_num_outputs="1">
            <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
            <param name="id_type" value="SYMBOL"/>
            <param name="organism" value="Gg"/>
            <param name="output_cols" value="GO,ENTREZID" />
            <output name="out_tab" file="out_gallus.tab" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

13:133f36c29579

    <description>annotate a generic set of identifiers</description>
    <xrefs>
        <xref type="bio.tools">annotatemyids</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">3.16.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>

        <test expect_num_outputs="1">
            <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
            <param name="id_type" value="ENSEMBL"/>
            <param name="organism" value="Hs"/>
            <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
            <output name="out_tab">
                <assert_contents>
                    <has_n_columns n="4"/>
                    <has_n_lines min="700"/>
                    <has_text_matching expression="ENSG00000012048" min="80"/>
                </assert_contents>
            </output>
        </test>
        <!-- Ensure duplicate Gene ID removal works -->
        <test expect_num_outputs="1">
            <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
            <param name="id_type" value="ENSEMBL"/>
            <param name="organism" value="Hs"/>
            <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
            <param name="remove_dups" value="True" />
            <output name="out_tab">
                <assert_contents>
                    <has_n_columns n="4"/>
                    <has_n_lines n="9"/>
                    <has_text_matching expression="ENSG00000012048" n="1"/>
                </assert_contents>
            </output>
        </test>
        <!-- Arabidopsis database -->
        <test expect_num_outputs="1">
            <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/>
            <param name="id_type" value="SYMBOL"/>
            <param name="organism" value="At"/>
            <param name="output_cols" value="GO,ENTREZID" />
            <output name="out_tab">
                <assert_contents>
                    <has_n_columns n="5"/>
                    <has_n_lines min="20"/>
                    <has_text_matching expression="CLE13" min="5"/>
                </assert_contents>
            </output>
        </test>
        <!-- Gallus gallus database -->
        <test expect_num_outputs="1">
            <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
            <param name="id_type" value="SYMBOL"/>
            <param name="organism" value="Gg"/>
            <param name="output_cols" value="GO,ENTREZID" />
            <output name="out_tab">
                <assert_contents>
                    <has_n_columns n="5"/>
                    <has_n_lines min="40"/>
                    <has_text_matching expression="TENM2" min="20"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark