example.xml

<tool id="example" name="example" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## vcf definition
#if $required_arguments.vcf:
   --vcf $required_arguments.vcf
#end if
## end vcf definition

## out definition
#if $required_arguments.out:
   --out $required_arguments.out
#end if
## end out definition

## vcftype definition
#if $optional_input_arguments.vcftype:
   --vcftype $optional_input_arguments.vcftype
#end if
## end vcftype definition

## samples definition
#if $optional_input_arguments.samples:
   --samples $optional_input_arguments.samples
#end if
## end samples definition

## period definition
#if $optional_input_arguments.period:
   --period $optional_input_arguments.period
#end if
## end period definition

## quality definition
#for $item in $quality_plot_options.quality:
      ## quality definition
   #if $item:
   --quality $item
   #end if
   ## end quality definition

#end for
## end quality definition

## quality_ignore_no_call definition
#if $quality_plot_options.quality_ignore_no_call:
   --quality-ignore-no-call $quality_plot_options.quality_ignore_no_call
#end if
## end quality_ignore_no_call definition

## refbias_metric definition
#if $reference_bias_plot_options.refbias_metric:
   --refbias-metric $reference_bias_plot_options.refbias_metric
#end if
## end refbias_metric definition

## refbias_mingts definition
#if $reference_bias_plot_options.refbias_mingts:
   --refbias-mingts $reference_bias_plot_options.refbias_mingts
#end if
## end refbias_mingts definition

## refbias_xrange_min definition
#if $reference_bias_plot_options.refbias_xrange_min:
   --refbias-xrange-min $reference_bias_plot_options.refbias_xrange_min
#end if
## end refbias_xrange_min definition

## refbias_xrange_max definition
#if $reference_bias_plot_options.refbias_xrange_max:
   --refbias-xrange-max $reference_bias_plot_options.refbias_xrange_max
#end if
## end refbias_xrange_max definition

## refbias_binsize definition
#if $reference_bias_plot_options.refbias_binsize:
   --refbias-binsize $reference_bias_plot_options.refbias_binsize
#end if
## end refbias_binsize definition

## numrecords definition
#if $debug_group.numrecords:
   --numrecords $debug_group.numrecords
#end if
## end numrecords definition

## version definition
#if $version.version:
   --version $version.version
#end if
## end version definition

    ]]></command>
    <inputs>
        <section name="required_arguments" title="Required arguments" expanded="true">
            <param argument="--vcf" type="text" optional="true" label="vcf" help="VCF file to analyze."/>
            <param argument="--out" type="text" optional="true" label="out" help="Output prefix for files generated"/>
        </section>

        <section name="optional_input_arguments" title="Optional input arguments" expanded="true">
            <param argument="--vcftype" type="select" optional="false" label="vcftype"
                   help="Which type of VCF to restrict the input to, or 'auto' for no restrction">
                <option value="##!!## Name trh could not be loaded">##!!## name trh could not be loaded</option>
            </param>
            <param argument="--samples" type="text" optional="false" label="samples"
                   help="File containing list of samples to include"/>
            <param argument="--period" type="integer" optional="false" label="period"
                   help="Only consider repeats with this motif length"/>
        </section>

        <section name="quality_plot_options" title="Quality plot options" expanded="true">
            <repeat name="quality_repeat" title="quality_repeat">
                <param argument="--quality" type="select" optional="false" label="quality"
                       help="Which quality plot(s) to produce. May be specified more than  once. See the README for more info">
                    <option value="per-locus">Per-locus</option>

                    <option value="sample-stratified">Sample-stratified</option>

                    <option value="per-sample">Per-sample</option>

                    <option value="locus-stratified">Locus-stratified</option>

                    <option value="per-call">Per-call</option>
                </param>
            </repeat>
            <param argument="--quality-ignore-no-call" type="text" optional="false" label="quality_ignore_no_call"
                   help="Exclude no-calls and calls without quality scores from quality graph distributions instead of the default, which is to include them as zero quality calls. Setting this can cause the plotting to crash if it reduces the number of valid calls (in a strata) to <= 1"/>
        </section>

        <section name="reference_bias_plot_options" title="Reference bias plot options" expanded="true">
            <param argument="--refbias-metric" type="select" optional="false" label="refbias_metric"
                   help="Which metric to use for the y-axis on the reference bias plot.">
                <option value="mean">Mean</option>

                <option value="median">Median</option>
            </param>
            <param argument="--refbias-mingts" type="integer" optional="false" label="refbias_mingts"
                   help="Don't compute points for the reference bias plot based on fewer than this many genotypes"/>
            <param argument="--refbias-xrange-min" type="integer" optional="false" label="refbias_xrange_min"
                   help="Minimum x-axis value (bp) to show on the reference bias plot"/>
            <param argument="--refbias-xrange-max" type="integer" optional="false" label="refbias_xrange_max"
                   help="Maximum x-axis value (bp) to show on the reference bias plot"/>
            <param argument="--refbias-binsize" type="integer" optional="false" label="refbias_binsize"
                   help="Size (bp) of x-axis bins for the reference bias plot"/>
        </section>

        <section name="debug_group" title="Debug group" expanded="true">
            <param argument="--numrecords" type="integer" optional="false" label="numrecords"
                   help="Only process this many records"/>
        </section>

        <section name="version" title="Version" expanded="true">
            <param argument="--version" type="text" optional="false" label="version"/>
        </section>

    </inputs>
    <outputs>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>