view gemini_query.xml @ 1:5fec0c2b77c7 draft

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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description></description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">query</token>
    </macros>
    <command>
<![CDATA[
        gemini @BINARY@

            #if $q.strip():
                -q "${q}"
            #end if

            #if $gt_filter.strip():
                --gt-filter "${gt_filter}"
            #end if

            #if $sample_filter.strip():
                --sample-filter "${sample_filter}"
            #end if

            $show_samples
            $show_families
            $family_wise
            $header
            $dgidb
            --in $in
            #if $region.strip():
                --region "${region}"
            #end if
            #if int($min_kindreds) > 0:
                --min-kindreds $min_kindreds
            #end if
            ##--format FORMAT       Format of output (JSON, TPED or default) # we will take default for the time being
            ##   --sample-delim STRING The delimiter to be used with the --show-samples option.




            "${ infile }"
            > "${ outfile }"
]]>
    </command>
                <!--
            ##TODO:
              - -carrier-summary-by-phenotype CARRIER_SUMMARY
                        Output columns of counts of carriers and non-carriers
                        stratified by the given sample phenotype column-->
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="sqlite" label="GEMINI database" />

        <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database"/>
        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values"/>
        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/>
        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/>

        <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" 
            label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>

        <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" 
            label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>

        <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" 
            label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>

        <expand macro="add_header_column" />

        <!-- TODO: is there any default values set? -->
        <param name="min_kindreds" size="4" type="integer" value="-1" lebel="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" />

        <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" 
            label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>

        <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
            <option value="all">all</option>
            <option value="none">none</option>
            <option value="any">any</option>
            <option value="only">only</option>
        </param>

        <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>


    </inputs>
    <outputs>
        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. 
The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants!

http://gemini.readthedocs.org/en/latest/content/querying.html

@CITATION@
    </help>
    <expand macro="citations"/>
</tool>