--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing_cgatools-982e19c29ec0/cgatools/tools/cgatools_1.6/snpdiff.xml	Thu Sep 27 13:37:59 2012 -0400
@@ -0,0 +1,198 @@
+<tool id="cg_snpdiff" name="snpdiff 1.6" version="1.0.1">
+<!--
+This tool creates a GUI for the snpdiff function of cgatools from Complete Genomics, Inc.
+written 6-18-2012 by bcrain@completegenomics.com
+updated 8-13-2012 by bcrain@completegenomics.com
+-->
+
+  <description>compares snp calls to var or masterVar file.</description> <!--adds description in toolbar-->
+
+  <command> <!--run executable-->
+<!-- print version of cgatools to STDOUT-->
+cgatools | head -1;
+
+<!-- print command lines to STDOUT-->
+echo "cgatools snpdiff 
+--reference $crr.fields.path 
+--variants $data_sources.varfile
+--genotypes $genotype
+--output-prefix cg_
+--reports `echo ${report1} ${report2} ${report3} | sed 's/  */,/g'` 
+";
+
+<!-- execute cgatools-->
+cgatools snpdiff 
+--reference $crr.fields.path 
+--variants $data_sources.varfile
+--genotypes $genotype
+--output-prefix cg_
+--reports `echo ${report1} ${report2} ${report3} | sed 's/  */,/g'` 
+
+  </command>
+
+  <outputs>
+  	<data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="${tool.name} Output">
+  	<filter>(report1 == 'Output')</filter>
+  	</data>
+  	<data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="${tool.name} Verbose">
+  	<filter>(report2 == 'Verbose')</filter>
+  	</data>
+  	<data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="${tool.name} Stats">
+  	<filter>(report3 == 'Stats')</filter>
+  	</data>
+  </outputs>
+  
+  <inputs>
+		<!--form field to select crr file-->
+		<param name="crr" type="select" label="Reference genome (.crr file)">
+			<options from_data_table="cg_crr_files" />
+		</param>
+	
+		<!--conditional to select data in/outside galaxy-->
+  	<conditional name="data_sources">
+      <param name="data_source" type="select" label="Where is the input var or masterVar file?">
+        <option value="in" selected="true">imported into Galaxy</option>
+        <option value="out">located outside Galaxy (data on server or mounted drive)</option>
+      </param>
+      
+			<!--form field to select input file-->
+      <when value="in">
+				<param name="varfile" type="data" format="cg_var,cg_mastervar" label="Var or masterVar file">
+					<validator type="dataset_ok_validator" />
+					<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+						metadata_name="dbkey" metadata_column="1"
+						message="cgatools is not currently available for this build."/>
+				</param>
+			</when>
+			
+			<!--form field to enter input file-->
+      <when value="out">
+				<param name="varfile" type="text" label="Var or masterVar file (/path/file)" size="40" help="Var or masterVar file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2">
+					<validator type="empty_field" message="You must supply a var or masterVar file"/>
+				</param>
+			</when>
+		</conditional>
+
+		<!--param to select genotypes file input-->
+		<param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at least the following columns: Chromosome, Offset0Based, Genotypes (Optional)">
+			<validator type="dataset_ok_validator" />
+			<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+				metadata_name="dbkey" metadata_column="1"
+				message="cgatools is not currently available for this build."/>
+			<!--<validator type="expression" message="Dataset does not match selected build.">value.dbkey == $crr.fields.dbkey</validator>-->
+		</param>
+
+		<!--params to select reports-->
+		<param name="report1" type="select" label="Create report Output">
+			<option value="">no</option>
+			<option value="Output" selected="true">yes</option>
+		</param>
+		<param name="report2" type="select" label="Create report Verbose">
+			<option value="">no</option>
+			<option value="Verbose">yes</option>
+		</param>
+		<param name="report3" type="select" label="Create report Stats">
+			<option value="">no</option>
+			<option value="Stats">yes</option>
+		</param>
+  </inputs>
+
+  <help>
+  
+**What it does**
+
+This tool ompares snp calls to a Complete Genomics variant file.
+
+**cgatools 1.6.0 Documentation**
+
+Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
+
+Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
+
+**Command line reference**::
+
+		COMMAND NAME
+		  snpdiff - Compares snp calls to a Complete Genomics variant file.
+		
+		DESCRIPTION
+		  Compares the snp calls in the "genotypes" file to the calls in a Complete 
+		  Genomics variant file. The genotypes file is a tab-delimited file with at 
+		  least the following columns (additional columns may be given):
+				
+		    Chromosome      (Required) The name of the chromosome.
+		    Offset0Based    (Required) The 0-based offset in the chromosome.
+		    GenotypesStrand (Optional) The strand of the calls in the Genotypes 
+		                    column (+ or -, defaults to +).
+		    Genotypes       (Optional) The calls, one per allele. The following 
+		                    calls are recognized:
+		                    A,C,G,T A called base.
+		                    N       A no-call.
+		                    -       A deleted base.
+		                    .       A non-snp variation.
+				
+		  The output is a tab-delimited file consisting of the columns of the 
+		  original genotypes file, plus the following additional columns:
+				
+		    Reference         The reference base at the given position.
+		    VariantFile       The calls made by the variant file, one per allele. 
+		                      The character codes are the same as is described for 
+		                      the Genotypes column.
+		    DiscordantAlleles (Only if Genotypes is present) The number of 
+		                      Genotypes alleles that are discordant with calls in 
+		                      the VariantFile. If the VariantFile is described as 
+		                      haploid at the given position but the Genotypes is 
+		                      diploid, then each genotype allele is compared 
+		                      against the haploid call of the VariantFile.
+		    NoCallAlleles     (Only if Genotypes is present) The number of 
+		                      Genotypes alleles that were no-called by the 
+		                      VariantFile. If the VariantFile is described as 
+		                      haploid at the given position but the Genotypes is 
+		                      diploid, then a VariantFile no-call is counted twice.
+				
+		  The verbose output is a tab-delimited file consisting of the columns of the
+		  original genotypes file, plus the following additional columns:
+				
+		    Reference   The reference base at the given position.
+		    VariantFile The call made by the variant file for one allele (there is 
+		                a line in this file for each allele). The character codes 
+		                are the same as is described for the Genotypes column.
+		    [CALLS]     The rest of the columns are pasted in from the VariantFile,
+		                describing the variant file line used to make the call.
+				
+		  The stats output is a comma-separated file with several tables describing 
+		  the results of the snp comparison, for each diploid genotype. The tables 
+		  all describe the comparison result (column headers) versus the genotype 
+		  classification (row labels) in different ways. The "Locus classification" 
+		  tables have the most detailed match classifications, while the "Locus 
+		  concordance" tables roll these match classifications up into "discordance" 
+		  and "no-call". A locus is considered discordant if it is discordant for 
+		  either allele. A locus is considered no-call if it is concordant for both 
+		  alleles but has a no-call on either allele. The "Allele concordance" 
+		  describes the comparison result on a per-allele basis.
+		
+		OPTIONS
+		  -h [ --help ] 
+		      Print this help message.
+		
+		  --reference arg
+		      The input crr file.
+		
+		  --variants arg
+		      The input variant file.
+		
+		  --genotypes arg
+		      The input genotypes file.
+		
+		  --output-prefix arg
+		      The path prefix for all output reports.
+		
+		  --reports arg (=Output,Verbose,Stats)
+		      Comma-separated list of reports to generate. A report is one of:
+		        Output  The output genotypes file.
+		        Verbose The verbose output file.
+		        Stats   The stats output file.
+						
+		SUPPORTED FORMAT_VERSION
+		  0.3 or later
+  </help>
+</tool>