comparison gemini_load.xml @ 6:b2c25142267e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 0d594bd114a5b090efd84449c4af74ef219c9646

5:b5b53c27baca

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

        <param argument="-p" name="ped" type="data" format="tabular" optional="True"
        label="Sample and family information in PED format"
        help="The pedigree dataset is optional, but several GEMINI tools require the relationship between samples (i.e., the family structure) and/or the sample phenotype to be defined. The PED format is a simple tabular format (see the tool help below for details). If you choose to not provide sample information now, but later find that you need it for your analysis, you can also add it to an existing GEMINI database by using the GEMINI amend tool." />
        <param name="opt_content" type="select" display="checkboxes" multiple="true" optional="true"
        label="Load the following optional content into the database"
        help="The preselected defaults should be ok for most use cases. If you are not interested in certain annotations, you can speed up database creation and decrease the resulting database size slightly by not loading them into the database. Note: GERP and CADD scores are optional parts of the annotation source and can only be loaded if available.">
            <option value="gerp_bp" selected="true">GERP scores</option>
            <option value="cadd" selected="true">CADD scores</option>
            <option value="gene_tables" selected="true">Gene tables</option>
            <option value="genotypes" selected="true">Sample genotypes</option>
            <option value="gt_pl" selected="true">Genotype likelihoods (sample PLs)</option>
            <option value="passonly" selected="false">only variants that passed all filters</option>
            <option value="info_string" selected="false">variant INFO field</option>

            <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**

Before we can use GEMINI to explore genetic variation, we must first load the
variant information stored in VCF format into the GEMINI database framework.

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>

        <param argument="-p" name="ped" type="data" format="tabular" optional="True"
        label="Sample and family information in PED format"
        help="The pedigree dataset is optional, but several GEMINI tools require the relationship between samples (i.e., the family structure) and/or the sample phenotype to be defined. The PED format is a simple tabular format (see the tool help below for details). If you choose to not provide sample information now, but later find that you need it for your analysis, you can also add it to an existing GEMINI database by using the GEMINI amend tool." />
        <param name="opt_content" type="select" display="checkboxes" multiple="true" optional="true"
        label="Load the following optional content into the database"
        help="The preselected defaults should be ok for most use cases (feel free to enable CADD scores for non-commercial use). If you are not interested in certain annotations, you can speed up database creation and decrease the resulting database size slightly by not loading them into the database. Note: GERP and CADD scores are optional parts of the annotation source and can only be loaded if available.">
            <option value="gerp_bp" selected="true">GERP scores</option>
            <option value="cadd" selected="false">CADD scores (non-commercial use only; see licensing note below)</option>
            <option value="gene_tables" selected="true">Gene tables</option>
            <option value="genotypes" selected="true">Sample genotypes</option>
            <option value="gt_pl" selected="true">Genotype likelihoods (sample PLs)</option>
            <option value="passonly" selected="false">only variants that passed all filters</option>
            <option value="info_string" selected="false">variant INFO field</option>

            <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**

CADD scores are freely available for non-commercial applications only. Make
sure you `contact the developers <https://cadd.gs.washington.edu/contact>`__
before using them in any commercial application.

-----

**What it does**

Before we can use GEMINI to explore genetic variation, we must first load the
variant information stored in VCF format into the GEMINI database framework.