view tools/sibelia/init_sibelia.xml @ 5:7b5e87542bd8 draft default tip

Coming to conclusion. Testing.

<tool id="Sibelia" name="sibelia">
  <command interpreter="python">
		#if $p_s.p_s_select == "-s" #Sibelia_wrapper.py -s  $p_s.simplification $ram -m $b_size $single_ou $postprocess -i $iter $fasta
		#else #Sibelia_wrapper.py -k  $p_s.cpfile $ram -m $b_size $single_ou $postprocess -i $iter $fasta
		#end if#
 </command>
  <inputs>
	<conditional name="p_s">
    <param name="p_s_select" type="select" label="Parameters set">
        <option value="-s">Select parameters set</option>
        <option value="-k">Custom parameteres set</option>
    </param>
    <when value="-k">
        <param name="cpfile" size="50" type="text" label="File of custom parameters set" />
    </when>
    <when value="-s">  
    	<param name="simplification" type="select" label="Simplification">
				<option value="loose">Loose</option>
				<option value="fine">Fine</option>
			</param>	
		</when>
	</conditional>
		<param name="ram" type="boolean" truevalue="-r" falsevalue="" label="Store temporary files in RAM?" />
		<param name="single_ou" type="boolean" truevalue="-a" falsevalue="" label="Find blocks that occur exactly once in each input sequence" />
		<param name="postprocess" type="boolean" truevalue="--nopostprocess" falsevalue="" label="Turn off postprocessing?" />
		<param name="iter" type="integer" value="4" label="Number of iterations" />
		<param name="b_size" type="integer" value="2000" label="Minimum block size" />
		<param name="fasta" size="50" type="text" label="Path to input fasta file" />
	</inputs>
  <outputs>
		<data format="txt" name="outperm" label="Genomes permutations" from_work_dir="genomes_permutations.txt" />
		<data format="txt" name="outblc" label="Blocks coords" from_work_dir="blocks_coords.txt" />
		<data format="txt" name="outcov" label="Coverage report" from_work_dir="coverage_report.txt" />
		<data format="html" name="outbld" label="Blocks diagram" from_work_dir="d3_blocks_diagram.html" />
	</outputs>
	<!-- <tests>
		<test>
			<param name="p_s_select" value="-s" />
			<param name="simplification" value="loose" />
			<param name="ram" value="0" />
			<param name="single_ou" value="0" />
			<param name="postprocess" value="0" />
			<param name="fasta" value="Helicobacter_pylori.fasta" />
		</test>
		<test>
			<param name="p_s_select" value="-k" />
			<param name="cpfile" value="CPFile.txt" />
			<param name="ram" value="0" />
			<param name="single_ou" value="0" />
			<param name="postprocess" value="0" />
			<param name="fasta" value="Helicobacter_pylori.fasta" />
		</test>
	</tests> -->
	<help>
		.. class:: infomark
		Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.
	</help>
</tool>