view candisnp.xml @ 8:191a144b007e draft default tip

Minor code changes.

<tool id="candisnp" name="candisnp">
	<description></description>
	<requirements>
	  <requirement type="package" version="2.7.4">python</requirement>
	  <requirement type="package" version="4.0">snpeff</requirement>
	</requirements>
	<command interpreter="python">candisnp.py 
		#if $snpDb.genomeSrc == 'cached':
		 --ref="${snpDb.genomeVersion.fields.key}"
		#end if
                $input
                $candisnp_html
	</command>


	<inputs>
		<param format="vcf" name="input" type="data" label="snpEff output"/>
		<conditional name="snpDb">
			<param name="genomeSrc" type="select" label="Genome source">
				<option value="cached">Locally installed reference genome</option>
			</param>
			<when value="cached">
				<param name="genomeVersion" type="select" label="Genome">
					<!-- GENOME DESCRIPTION -->
					<options from_data_table="snpeffv_genomedb">
						<!-- <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> -->
						<filter type="unique_value" column="2"/>
					</options>
				</param>
			</when>
		</conditional>			
	</inputs>
	<outputs>
		<data format="html" name="candisnp_html" label="${tool.name}" />
	</outputs>

	<help>
	A tool to pull in visualisation output from CandiSNP (candisnp.tsl.ac.uk).
	</help>
</tool>