comparison gemini_load.xml @ 7:64132aa2d62a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"

6:b2c25142267e

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1">
    <description>Loading a VCF file into GEMINI</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">load</token>
    </macros>

    <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":

            '$outfile'
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="vcf"
        label="VCF dataset to be loaded in the GEMINI database"
        help="Only build 37 (aka hg19) of the human genome is supported.">
            <options>
                <filter type="add_value" value="hg19" />
                <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />

            <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

**CADD scores licensing**

7:64132aa2d62a

<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="version_command" />
    <command>
<![CDATA[
        @PROVIDE_ANNO_DATA@

        ## gemini load expects a bgzipped and tabixed vcf as input
        #set $tabixed_file = 'input.vcf.gz'
        #if $infile.ext == 'vcf':
            bgzip -c '$infile' > $tabixed_file &&
            tabix -p vcf $tabixed_file &&
        #else:
            ln -s '$infile' $tabixed_file &&
            ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi &&
        #end if

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

            '$outfile'
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="vcf,vcf_bgzip"
        label="VCF dataset to be loaded in the GEMINI database"
        help="Only build 37 (aka hg19) of the human genome is supported.">
            <options>
                <filter type="add_value" value="hg19" />
                <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />

            <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

**CADD scores licensing**