CanSNPer.xml

<tool id="CanSNPer" name="CanSNPer genotyping">
	<description>Galaxy interface for CanSNPer</description>
	<command interpreter="python">CanSNPer -d --galaxy $verbosity -i $file -r $organism > $outfile1 2> $outfile2</command>
	<inputs>
		<param name="organism" type="text" size="30" label="Reference organism name"/>
		<param format="fasta" name="file" type="data" label="Fasta file"/>
		<param name="verbosity" type="select" label="Verbosity">
			<option value="">Normal</option>
			<option value="-v">Verbose</option>
			<option value="-vq">Developer</option>
		</param>
	</inputs>
	<outputs>
		<data from_work_dir="CanSNPer_tree_galaxy.pdf" format="pdf" name="savetreefile" label="CanSNPer pdf tree"/>
		<data format="tabular" name="outfile1" label="CanSNPer output file"/>
		<data format="tabular" name="outfile2" label="CanSNPer error file"/>
	</outputs>
	<requirements>
		<requirement type="python-module">ete2</requirement>
		<requirement type="binary">progressiveMauve</requirement>
	</requirements>
	<help>
	This tool runs CanSNPer typing on uploaded fasta file.
	</help>
</tool>