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author dereeper
date Wed, 11 Sep 2013 09:08:15 -0400
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<tool id="SNiPloid" name="SNiPloid">
	<description>Comparison of SNP between a Tetraploid and its Parental Genomes</description>
	<command interpreter="bash">./SNiPloid.sh 
	$Poly_Analysis.polyornot <!-- $1 -->
	#if $Poly_Analysis.polyornot == "poly":
		
		$Poly_Analysis.depthPolyploid1 $Poly_Analysis.depthPolyploid2 	<!-- $4 $5 -->
		$Poly_Analysis.VCFpolyploid1 $Poly_Analysis.DOCpolyploid1 		<!-- $6 $7 -->
		$Poly_Analysis.VCFpolyploid2 $Poly_Analysis.DOCpolyploid2 		<!-- $8 $9 -->
	#else:
		$Poly_Analysis.Reference.ref <!-- $2 -->
		
		#if $Poly_Analysis.Reference.ref == "1":
			$Poly_Analysis.Reference.genome2Name
		#end if
		
		$Poly_Analysis.Reference.depthPolyploid1 $Poly_Analysis.Reference.depthGenome1					<!-- $6 $7 -->
		$Poly_Analysis.Reference.VCFpolyploid1 $Poly_Analysis.Reference.DOCpolyploid1						<!-- $8 $9 -->
		$Poly_Analysis.Reference.VCFgenome1 $Poly_Analysis.Reference.DOCgenome1						<!-- $10 $11 -->
		#if $Poly_Analysis.Reference.ref == "0":
			$Poly_Analysis.Reference.depthGenome2																			<!-- $12 -->
			$Poly_Analysis.Reference.VCFgenome2 $Poly_Analysis.Reference.DOCgenome2					<!-- $13 $14 -->
		#end if
	#end if
	$SNP_csv $SNP_html $SNP_count $SNP_count_csv $enableLowQuality $log
	#if $Poly_Analysis.polyornot == "poly":
		$Poly_Analysis.value_filter_p1 $Poly_Analysis.value_filter_p2
	#end if
	#if $annotation.add_annot == "yes":
		$annotation.add_annot $annotation.annotation_file $map
	#end if
	</command>
	
	<inputs>

		<conditional name="Poly_Analysis">
		
			<param type="select" name="polyornot" label="Type of analysis">
    	   		<option value="poly" selected="True">POLYPLOID vs POLYPLOID</option>
				<option value="notpoly">POLYPLOID vs PARENTAL DIPLOID GENOMES</option>
   			</param>

			<when value="poly">
				<param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid 1)" value="20"/>
				<param type="text" name="depthPolyploid2" label="Minimum read depth at a position to make a call (Polyploid 2)" value="20"/>
				<param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid 1)"/>
				<param format="vcf" name="VCFpolyploid2" type="data" label="VCF file (Polyploid 2)"/>
				<param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid 1)"/>
				<param format="coverage" name="DOCpolyploid2" type="data" label="Depth of coverage information (Polyploid 2)"/>
				<param type="text" name="value_filter_p1" label="Minimum minor allele frequency (in %) (Polyploid 1)" value="10"/>
				<param type="text" name="value_filter_p2" label="Minimum minor allele frequency (in %) (Polyploid 2)" value="10"/>
			</when>

			<when value="notpoly">
				<conditional name="Reference">
				
					<param type="select" name="ref" label="Reference" help="INTERN (Genome 2 as reference) or EXTERN">
						<option value="1" selected="True">INTERN</option>
						<option value="0">EXTERN</option>
					</param>

					<when value="0">
						<param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
						<param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
						<param type="text" name="depthGenome2" label="Minimum read depth at a position to make a call (Genome 2)" value="20"/>
						<param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
						<param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)"/>
						<param format="vcf" name="VCFgenome2" type="data" label="VCF file (Genome 2)"/>
						<param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
						<param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
						<param format="coverage" name="DOCgenome2" type="data" label="Depth of coverage information (Genome2)"/>
					</when>

					<when value="1">
						<param type="text" name="genome2Name" label="Genome 2 Name (Reference)" value="GenomeName"/>
						<param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
						<param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
						<param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
						<param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)" help="VCF file with [Genome 1] vs. [Genome 2] as Reference. /!\ Lost of heterozygosity for [Genome 2]"/>
						<param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
						<param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
					</when>

				</conditional>

			</when>

		</conditional>

		<conditional name="annotation">
            		<param name="add_annot" type="select" label="Add a genome annotation file">
              			<option value="no" selected="True">No annotation available</option>
		                <option value="yes">Add a genome annotation</option>
            		</param>
            		<when value="yes">
				<param format="gff3" name="annotation_file" type="data" label="Enter a genome annotation in GFF3 format"/>
            		</when>
	                <when value="no">
            		</when>
	        </conditional>	

		<param name="enableLowQuality" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Enable LowQual SNP ?" help="Default : only PASS SNP are considered" />
   		
		
	</inputs>
	
	<outputs>
	
		<data format="txt" name="SNP_csv" label="SNP output" />
		<data format="html" name="SNP_html" label="SNP output (HTML)" />
		<data format="html" name="SNP_count" label="Synthesis output (HTML)" />
		<data format="txt" name="SNP_count_csv" label="Synthesis output" />
		<data format="txt" name="log" label="log" />
		<data format="png" name="map" label="map" />
	</outputs>
	
	<help>
.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**

.. class:: infomark

**SNiPlay utilities**

-----

==============
 Authors:
==============

**Marine Peralta, Alexis Dereeper**

-----

==========
 Overview
==========

SNiPloid compares SNP between a tetraploid and its parental genomes, or between two polyploids.

-----

For further informations, please visite the website of the SNiPloid_ software.


.. _SNiPloid: http://sniplay.cirad.fr/cgi-bin/sniploid.cgi


	</help>

</tool>