comparison gemini_pathways.xml @ 4:69b5327a1f88 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

3:6b09debcfc49

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Map genes and variants to KEGG pathways</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">pathways</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini
            #if $annotation_databases:
                --annotation-dir "${annotation_databases.fields.path}"
            #end if
            @BINARY@
            -v $ensembl
            $lof
            "${ infile }"
            > "${ outfile }"

    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
            <param name="ensembl" value="68" />
            <output name="outfile" file="gemini_pathways_result.tabular" />
        </test>
    </tests>
    <help>
**What it does**

4:69b5327a1f88

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>Map genes and variants to KEGG pathways</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">pathways</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        @PROVIDE_ANNO_DATA@

        gemini
            @BINARY@
            -v $ensembl
            $lof
            "${ infile }"
            > "${ outfile }"

    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <param name="ensembl" value="68" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**