--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DC_Genotyper.xml	Sat Sep 27 05:38:17 2014 -0400
@@ -0,0 +1,83 @@
+<tool id="DC_Genotyper" name="DC Genotyper" version='0.0.1'>
+	<description></description>
+	<requirements>
+		<requirement type='package' version='3.0.2'>R_3_0_2</requirement>
+		<requirement type='package' version='0.1.18'>samtools</requirement>
+		<requirement type='package' version='0.2.6'>tabix</requirement>
+		<requirement type='package' version='latest'>blat_server</requirement>
+		<requirement type='package' version='1.92'>perl_module_threads</requirement>
+		<requirement type='package' version='1.46'>perl_module_threads_shared</requirement>
+		<requirement type='package' version='3.02'>perl_module_Thread_Queue</requirement>
+		<requirement type='package' version='2.3.32'>igvtools</requirement>
+        </requirements>
+	<command interpreter="perl">DC_Genotyper.pl 
+		-t "$targets" 
+		-b "$bamfile" 
+		-R "${ref.fields.path}" 
+		-p  "\${GALAXY_SLOTS:-4}"
+		#if $dbsnp.source == "history":
+			-s "${dbsnp.ownFile}"
+		#else 
+			-s "${dbsnp.indices.fields.path}"
+		#end if 
+		-m $mincov
+		-P $ploidy
+		
+		-a $output1 
+		-v $output2 
+	</command>	
+
+	<inputs>
+		<param  name="bamfile" type="data" format="bam" label="Sample BAM file" />
+		<param  name="targets" type="data" format="bed" label="Enrichment BED file" /> 
+		<param name="ref" type="select" label="Select a reference genome">
+          		<options from_data_table="DC_Genotyper_indexes">
+            		  <filter type="sort_by" column="2" />
+            		    <validator type="no_options" message="No indexes are available" />
+          		</options>
+        	</param>
+		<conditional name="dbsnp">
+		  <param name="source" type="select" label="Will you select a dbSNP file from your history, or use a built in version (which is faster)">
+			<option value="indexed">Use a built-in version</option>
+			<option value="history">Use one from the history</option>
+		  </param>
+		  <when value="indexed">
+			 <param name="indices" type="select" label="Select a dbSNP version">
+          		 	<options from_data_table="dbsnp_indexes">
+                         		<filter type="sort_by" column="2" />
+            				<validator type="no_options" message="No indexes are available" />
+          			</options>
+        		</param>
+		  </when>
+                  <when value="history">
+			<param name="ownFile" type="data" format="vcf,bcf" label="Select a dbSNP file from history"/>
+		  </when>
+          	</conditional>
+		<param name="mincov" value="400" type="integer" label="Minimal Coverage Depth" />
+		<param name="ploidy" type="integer" value='10' label="Expected Sample Ploidy" />
+	</inputs>
+	
+	<outputs>
+		<data format='txt' name="output1" label="${tool.name} on ${on_string}: Allele Fraction Distributions"/>
+		<data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file" />
+	</outputs>
+<help>
+
+**What it does**
+
+	1. get allele counts on all positions in specified targets (bed) using igvtools. Only SNPs !!
+	2. remove known dbsnp positions (bcf file)
+	3. Get distribution of background noise (pcr/sequencing errors), by modelling allele fractions as normal distributions.
+	4. Based on these distributions, check each position for significant change from the reference allele (based on allele fraction)
+	5. For abberant positions, check each alternate allele to see if it passes the background signal. 
+	6. Generate VCF file. 
+
+
+**Information**
+
+This tools is created by Geert Vandeweyer. It is a very early version with several limitations. Current limitations are : no support for indels, no plotting of the noise-models, incorrect syntax in for multi-allelic sites in the VCF file.
+
+Any feedback is welcome. 
+
+</help>
+</tool>