--- a/tool_dependencies.xml	Wed Jul 10 17:23:45 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcftools" version="0.1.11">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/vcftools/files/vcftools_0.1.11.tar.gz</action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">PREFIX="$INSTALL_DIR/vcftools make install</action>                
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/vcftools/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project
-        </readme>
-    </package>
-    
-</tool_dependency>

--- a/vcftools.xml	Wed Jul 10 17:23:45 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<toold id="vcftools" name="VCFtools" version="0.0.1">
-	<description>
-		The vcftools program is intended for analysis of diploid SNP data in VCF format.
-	</description>
-	<requirements>
-		<requirement type="package" version="0.1.11">vcftools</requirement>
-	</requirements>
-	<command>
-		vcftools
-
-		#if str($basic) == "gzvcf"
-			--gzvcf
-		#elif str($basic) == "bcf"
-			--bcf
-		#else 
-			--vcf
-		#end if
-
-		$input
-
-		#for $chromosome in $chr
-			--chr $chromosome.number
-		#end for
-
-		#for $chromosome in $notchr
-			--notchr $chromosome.number
-		#end for
-
-		#if str($frombp) != ""
-			--from-bp $frombp
-		#end if
-
-		#if str($tobp) != ""
-			--to-bp $tobp
-		#end if
-
-		#for $snp in $snps
-			--snp $snp.id
-		#end for
-
-		#if str(${snpfile.file_name}) != ""
-			--snps $snpfile
-		#end if
-
-		#if str(${excludesnpfile.file_name}) != ""
-			--snps $excludesnpfile
-		#end if
-
-		#if str($indels) == "keeponlyindels"
-			--keep-only-indels
-		#elif str($indels) == "removeindels"
-			--removeindels
-		#end if
-
-		$removefilterall $recodetostream > out.recode.vcf
-	</command>
-	<inputs>
-		<param name="input" type="data" label="Input vcf file" format="vcf" />
-		<param name="basic" type="select" label="Basic Options" value="vcf">
-			<option value="vcf">Decompressed vcf file (default)</option>
-			<option value="gzvcf">Compressed (gzipped) vcf file</option>
-			<option value="bcf">Compressed (bgzf) bcf file</option
-		</param>
-		<repeat name="chr" title="Include chromosomes to be processed">
-			<param name="number" label="Chromosome number" type="integer" optional="true" />
-		</repeat>
-		<repeat name="notchr" title="Exclude chromosomes from processing">
-			<param name="number" label="Chromosome number" type="integer" optional="true" />
-		</repeat>
-		<param name="frombp" label="Beginning of range to be processed" help="only if chromosomes are included. You must also specify the end of range to be processed." optional="true" type="integer"/>
-		<param name="tobp" label="End of range to be processed" optional="true" type="integer" help="only if chromosomes are included. You must also specify the beginning of range to be processed."/>
-		<repeat name="snps" title="SNPs to include">
-			<param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/>
-		</repeat>t
-		<param name="snpfile" type="data" format="txt, tabular" label="List of SNPs to include" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
-		<param name="excludesnpfile" type="data" label = "List of SNPs to disclude" format="txt, tabular" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
-		<param name="indels" type="select" label="Indel options" value="none">
-			<option value="keeponlyindels">Keep only indels</option>
-			<option value="removeindels"> Remove indels</option>
-		</param>
-		<param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
-		<param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
-	</inputs>
-	<outputs>
-		<data format="vcf" name="output" from_work_dir="out.recode.vcf">
-	</outputs>
-	<help>
-		Welcome to VCFtools - a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. More information at http://vcftools.sourceforge.net/index.html.
-	</help>
-