gemini query

            --in "${in}"

            #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
            #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.

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

            "${ infile }"
            > "${ outfile }"