comparison gemini_load.xml @ 9:2270a8b83c12 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd

8:45296e47d565

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
    <description>Loading a VCF file into GEMINI</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">load</token>
    </macros>
    <expand macro="requirements" />

    <tests>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
            <assert_command>
                <has_text text="--skip-gerp-bp" />
                <has_text text="--skip-cadd" />
                <not_has_text text="--skip-gene-tables" />
                <not_has_text text="--skip-pls" />

        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <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>
            <assert_command>

        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="genotypes,gt_pl" />
            <param name="has_genotypes" value="False" />
            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
            <assert_command>
                <has_text text="--skip-gerp-bp" />
                <has_text text="--skip-cadd" />
                <has_text text="--skip-gene-tables" />
                <not_has_text text="--skip-pls" />

            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <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>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <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[
.. class:: Warning mark

9:2270a8b83c12

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
    <description>Loading a VCF file into GEMINI</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">load</token>
    </macros>
    <expand macro="requirements" />

    <tests>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
            <assert_command>
                <has_text text="--skip-gerp-bp" />
                <has_text text="--skip-cadd" />
                <not_has_text text="--skip-gene-tables" />
                <not_has_text text="--skip-pls" />

        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
            <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>
            <assert_command>

        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
            <param name="opt_content" value="genotypes,gt_pl" />
            <param name="has_genotypes" value="False" />
            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
            <assert_command>
                <has_text text="--skip-gerp-bp" />
                <has_text text="--skip-cadd" />
                <has_text text="--skip-gene-tables" />
                <not_has_text text="--skip-pls" />

            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <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="20000" />
        </test>
        <test>
            <param name="annotation_databases" value="1999-01-01" />
            <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
            <param name="has_genotypes" value="True" />
            <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="20000" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: Warning mark