comparison gemini_load.xml @ 4:5c5cdbdc3534 draft

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

3:cf61daf064fe

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Loading a VCF file into GEMINI</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">load</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        ln -s "${ infile }" input.vcf &&
        bgzip -c input.vcf > input.vcf.gz &&
        tabix -p vcf input.vcf.gz &&

        gemini
            #if $annotation_databases:
                --annotation-dir "${annotation_databases.fields.path}"
            #end if
            @BINARY@
            -v input.vcf.gz
            #if str( $annotation_type ) != "None":
                -t "$annotation_type"
            #end if

    <outputs>
        <data name="outfile" format="gemini.sqlite" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="skip_gene_tables" value="True" />
            <param name="skip_gerp_bp" value="True" />
            <param name="skip_cadd" value="True" />
            <param name="no_genotypes" value="True" />
            <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

4:5c5cdbdc3534

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>Loading a VCF file into GEMINI</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">load</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        @PROVIDE_ANNO_DATA@

        ln -s "${ infile }" input.vcf &&
        bgzip -c input.vcf > input.vcf.gz &&
        tabix -p vcf input.vcf.gz &&

        gemini
            @BINARY@
            -v input.vcf.gz
            #if str( $annotation_type ) != "None":
                -t "$annotation_type"
            #end if

    <outputs>
        <data name="outfile" format="gemini.sqlite" />
    </outputs>
    <tests>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="skip_gene_tables" value="False" />
            <param name="skip_gerp_bp" value="True" />
            <param name="skip_cadd" value="True" />
            <param name="no_genotypes" value="False" />
            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
        </test>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="skip_gene_tables" value="False" />
            <param name="skip_gerp_bp" value="False" />
            <param name="skip_cadd" value="False" />
            <param name="no_genotypes" value="False" />
            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
            <assert_stderr>
                <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
                <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
            </assert_stderr>
        </test>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="skip_gene_tables" value="True" />
            <param name="skip_gerp_bp" value="True" />
            <param name="skip_cadd" value="True" />
            <param name="no_genotypes" value="True" />
            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
        </test>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
            <param name="skip_gene_tables" value="False" />
            <param name="skip_gerp_bp" value="True" />
            <param name="skip_cadd" value="True" />
            <param name="no_genotypes" value="False" />
            <param name="ped" value="gemini_amend.ped" ftype="tabular" />
            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**