# HG changeset patch
# User bcrain-completegenomics
# Date 1339695888 14400
# Node ID e59abf6c3d0b801dd7b98c398d77a40e25c57845
# Parent  0fedca1d0d1e7786484e6bb373628ea088b0d16d
Uploaded

diff -r 0fedca1d0d1e -r e59abf6c3d0b calldiff.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/calldiff.xml	Thu Jun 14 13:44:48 2012 -0400
@@ -0,0 +1,343 @@
+<tool id="cga_calldiff" name="calldiff(beta)" version="0.0.1">
+
+  <description>compares 2 Complete Genomics variant files.</description> <!--adds description in toolbar-->
+
+  <requirements>
+  	<requirement type="binary">cgatools</requirement>
+  </requirements>
+
+  <command> <!--run executable-->
+  	cgatools calldiff --beta
+  	--reference ${crr.fields.path}
+		--variantsA $data_sources.inputA
+		--variantsB $data_sources.inputB
+		$validation 
+		$diploid 
+		--locus-stats-column-count $column 
+		--max-hypothesis-count $hypothesis
+		--output-prefix cg_
+		--reports `echo ${report1} ${report2} ${report3} ${report4} ${report5} ${somatic.report6} | sed 's/  */,/g'` 
+		#if $somatic.report6 == "SomaticOutput"
+			--genome-rootA $somatic.genomeA
+			--genome-rootB $somatic.genomeB
+			--calibration-root $somatic.calibration
+		#end if
+  </command>
+
+  <outputs>
+  	<data format="tabular" name="output1" from_work_dir="cg_SuperlocusOutput.tsv" label="${tool.name} on ${on_string}: SuperlocusOutput">
+  	<filter>(report1 == 'SuperlocusOutput')</filter>
+  	</data>
+  	<data format="tabular" name="output2" from_work_dir="cg_SuperlocusStats.tsv" label="${tool.name} on ${on_string}: SuperlocusStats">
+  	<filter>(report2 == 'SuperlocusStats')</filter>
+  	</data>
+  	<data format="tabular" name="output3" from_work_dir="cg_LocusOutput.tsv" label="${tool.name} on ${on_string}: LocusOutput">
+  	<filter>(report3 == 'LocusOutput')</filter>
+  	</data>
+  	<data format="tabular" name="output4" from_work_dir="cg_LocusStats.tsv" label="${tool.name} on ${on_string}: LocusStats">
+  	<filter>(report4 == 'LocusStats')</filter>
+  	</data>
+  	<data format="tabular" name="output5a" from_work_dir="cg_VariantsA.tsv" label="${tool.name} on ${on_string}: VariantsA">
+  	<filter>(report5 == 'VariantOutput')</filter>
+  	</data>
+  	<data format="tabular" name="output5b" from_work_dir="cg_VariantsB.tsv" label="${tool.name} on ${on_string}: VariantsB">
+  	<filter>(report5 == 'VariantOutput')</filter>
+  	</data>
+  	<data format="tabular" name="output6" from_work_dir="cg_SomaticOutput.tsv" label="${tool.name} on ${on_string}: SomaticOutput">
+  	<filter>(somatic['report6'] == 'SomaticOutput')</filter>
+  	</data>
+  </outputs>
+  
+  <inputs>
+		<!--form field to select crr file-->
+		<param name="crr" type="select" label="Genome build">
+			<options from_data_table="cg_crr_files" />
+		</param>
+	
+		<!--conditional to select variant file input-->
+  	<conditional name="data_sources">
+      <param name="data_source" type="select" label="Where are the input varfiles?">
+        <option value="in" selected="true">imported into Galaxy</option>
+        <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
+      </param>
+      <when value="in">
+				<!--form field to select variant files-->
+				<param name="inputA" type="data" format="cg_var" label="Dataset A">
+					<validator type="unspecified_build" />
+					<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>
+				<param name="inputB" type="data" format="cg_var" label="Dataset B">
+					<validator type="unspecified_build" />
+					<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>
+      <when value="out">
+				<!--form field to select crr file-->
+				<param name="inputA" type="text" label="Variant file A (path/file_name)" size="300" help="Variant files can be compressed (gz, bz2)."/>
+				<param name="inputB" type="text" label="Variant file B (path/file_name)" size="300" help="Variant files can be compressed (gz, bz2)."/>
+			</when>
+		</conditional>
+		
+		<param name="diploid" type="select" label="Use diploid variant model" help="Uses varScoreEAF instead of varScoreVAF in somatic score computations. Also, uses diploid variant model instead of variable allele mixture model.">
+			<option value="">no</option>
+			<option value="--diploid">yes</option>
+		</param>
+			
+		<param name="column" type="integer" label="Number of columns for locus compare classification in the locus stats file (default 15)" value="15"/>
+		
+		<param name="hypothesis" type="integer" label="Maximum number of possible phasings to consider for a superlocus (default 32)" value="32"/>
+		      
+		<param name="validation" type="select" label="Reference cover validation" help="Turns on/off validation that all bases of a chromosome are covered by calls of the variant file.">
+			<option value="">on</option>
+			<option value="--no-reference-cover-validation">off</option>
+		</param>
+			
+		<param name="report1" type="select" label="Report SuperlocusOutput">
+			<option value="">no</option>
+			<option value="SuperlocusOutput">yes</option>
+		</param>
+		<param name="report2" type="select" label="Report SuperlocusStats">
+			<option value="">no</option>
+			<option value="SuperlocusStats">yes</option>
+		</param>
+		<param name="report3" type="select" label="Report LocusOutput">
+			<option value="">no</option>
+			<option value="LocusOutput">yes</option>
+		</param>
+		<param name="report4" type="select" label="Report LocusStats">
+			<option value="">no</option>
+			<option value="LocusStats">yes</option>
+		</param>
+		<param name="report5" type="select" label="Report VariantOutput" help="Both variant files annotated by comparison results.If the somatic output report is requested, file A is also annotated with the same score ranks as produced in that report.">
+			<option value="">no</option>
+			<option value="VariantOutput">yes</option>
+		</param>
+		
+		<conditional name="somatic">
+			<param name="report6" type="select" label="Report SomaticOutput" help="This report can only be generated on local Galaxy instances. Report for the list of simple variations that are present only in file 'A', annotated with the score that indicates the probability of the variation being truly somatic. Note: generating this report slows calldiff by 10x-20x.">
+				<option value="">no</option>
+				<option value="SomaticOutput">yes</option>
+			</param>
+			<when value="SomaticOutput">
+				<param name="genomeA" type="text" size="300" label="Directory for genome A (/path/dir)" help="The 'A' genome directory, for example /data/GS00118-DNA_A01; this directory is expected to contain ASM/REF and ASM/EVIDENCE subdirectories."/>
+				<param name="genomeB" type="text" size="300" label="Directory for genome B (/path/dir)" help="The 'B' genome directory"/>
+				<param name="calibration" type="text" size="300" label="Directory calibration data (/path/dir)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v1.tgz"/>
+			</when>
+		</conditional>
+		
+  </inputs>
+
+  <help>
+  
+**What it does**
+
+This tool compares two Complete Genomics variant files.
+
+cgatools: http://sourceforge.net/projects/cgatools/files/
+
+-----
+
+**cgatools Manual**::
+
+		COMMAND NAME
+		  calldiff - Compares two Complete Genomics variant files.
+		
+		DESCRIPTION
+		  Compares two Complete Genomics variant files. Divides the genome up into 
+		  superloci of nearby variants, then compares the superloci. Also refines the
+		  comparison to determine per-call or per-locus comparison results.
+				
+		  Comparison results are usually described by a semi-colon separated string, 
+		  one per allele. Each allele's comparison result is one of the following 
+		  classifications:
+				
+		    ref-identical   The alleles of the two variant files are identical, and
+		                    they are consistent with the reference.
+		    alt-identical   The alleles of the two variant files are identical, and
+		                    they are inconsistent with the reference.
+		    ref-consistent  The alleles of the two variant files are consistent, 
+		                    and they are consistent with the reference.
+		    alt-consistent  The alleles of the two variant files are consistent, 
+		                    and they are inconsistent with the reference.
+		    onlyA           The alleles of the two variant files are inconsistent, 
+		                    and only file A is inconsistent with the reference.
+		    onlyB           The alleles of the two variant files are inconsistent, 
+		                    and only file B is inconsistent with the reference.
+		    mismatch        The alleles of the two variant files are inconsistent, 
+		                    and they are both inconsistent with the reference.
+		    phase-mismatch  The two variant files would be consistent if the 
+		                    hapLink field had been empty, but they are 
+		                    inconsistent.
+		    ploidy-mismatch The superlocus did not have uniform ploidy.
+				
+		  In some contexts, this classification is rolled up into a simplified 
+		  classification, which is one of "identical", "consistent", "onlyA", 
+		  "onlyB", or "mismatch".
+				
+		  A good place to start looking at the results is the superlocus-output file.
+		  It has columns defined as follows:
+				
+		    SuperlocusId   An identifier given to the superlocus.
+		    Chromosome     The name of the chromosome.
+		    Begin          The 0-based offset of the start of the superlocus.
+		    End            The 0-based offset of the base one past the end of the 
+		                   superlocus.
+		    Classification The match classification of the superlocus.
+		    Reference      The reference sequence.
+		    AllelesA       A semicolon-separated list of the alleles (one per 
+		                   haplotype) for variant file A, for the phasing with the 
+		                   best comparison result.
+		    AllelesB       A semicolon-separated list of the alleles (one per 
+		                   haplotype) for variant file B, for the phasing with the 
+		                   best comparison result.
+				
+		  The locus-output file contains, for each locus in file A and file B that is
+		  not consistent with the reference, an annotated set of calls for the locus.
+		  The calls are annotated with the following columns:
+				
+		    SuperlocusId            The id of the superlocus containing the locus.
+		    File                    The variant file (A or B).
+		    LocusClassification     The locus classification is determined by the 
+		                            varType column of the call that is inconsistent
+		                            with the reference, concatenated with a 
+		                            modifier that describes whether the locus is 
+		                            heterozygous, homozygous, or contains no-calls.
+		                            If there is no one variant in the locus (i.e., 
+		                            it is heterozygous alt-alt), the locus 
+		                            classification begins with "other".
+		    LocusDiffClassification The match classification for the locus. This is
+		                            defined to be the best of the comparison of the
+		                            locus to the same region in the other file, or 
+		                            the comparison of the superlocus.
+				
+		  The somatic output file contains a list of putative somatic variations of 
+		  genome A. The output includes only those loci that can be classified as 
+		  snp, del, ins or sub in file A, and are called reference in the file B. 
+		  Every locus is annotated with the following columns:
+				
+		    VarCvgA                 The totalReadCount from file A for this locus 
+		                            (computed on the fly if file A is not a 
+		                            masterVar file).
+		    VarScoreA               The varScoreVAF from file A, or varScoreEAF if 
+		                            the "--diploid" option is used.
+		    RefCvgB                 The maximum of the uniqueSequenceCoverage 
+		                            values for the locus in genome B.
+		    RefScoreB               Minimum of the reference scores of the locus in
+		                            genome B.
+		    SomaticCategory         The category used for determining the 
+		                            calibrated scores and the SomaticRank.
+		    VarScoreACalib          The calibrated variant score of file A, under 
+		                            the model selected by using or not using the 
+		                            "--diploid" option, and corrected for the count
+		                            of heterozygous variants observed in this 
+		                            genome. See user guide for more information.
+		    VarScoreBCalib          The calibrated reference score of file B, under
+		                            the model selected by using or not using the 
+		                            "--diploid" option, and corrected for the count
+		                            of heterozygous variants observed in this 
+		                            genome. See user guide for more information.
+		    SomaticRank             The estimated rank of this somatic mutation, 
+		                            amongst all true somatic mutations within this 
+		                            SomaticCategory. The value is a number between 
+		                            0 and 1; a value of 0.012 means, for example, 
+		                            that an estimated 1.2% of the true somatic 
+		                            mutations in this somaticCategory have a 
+		                            somaticScore less than the somaticScore for 
+		                            this mutation. See user guide for more 
+		                            information.
+		    SomaticScore            An integer that provides a total order on 
+		                            quality for all somatic mutations. It is equal 
+		                            to -10*log10( P(false)/P(true) ), under the 
+		                            assumption that this genome has a rate of 
+		                            somatic mutation equal to 1/Mb for 
+		                            SomaticCategory snp, 1/10Mb for SomaticCategory
+		                            ins, 1/10Mb for SomaticCategory del, and 1/20Mb
+		                            for SomaticCategory sub. The computation is 
+		                            based on the assumptions described in the user 
+		                            guide, and is affected by choice of variant 
+		                            model selected by using or not using the 
+		                            "--diploid" option.
+		    SomaticQuality          Equal to VQHIGH for all somatic mutations where
+		                            SomaticScore &gt;= -10. Otherwise, this column is 
+		                            empty.
+				
+		OPTIONS
+		  -h [ --help ] 
+		      Print this help message.
+		
+		  --reference arg
+		      The input crr file.
+		
+		  --variantsA arg
+		      The "A" input variant file.
+		
+		  --variantsB arg
+		      The "B" input variant file.
+		
+		  --output-prefix arg
+		      The path prefix for all output reports.
+		
+		  --reports arg (=SuperlocusOutput,SuperlocusStats,LocusOutput,LocusStats)
+		      Comma-separated list of reports to generate. (Beware any reports whose 
+		      name begins with "Debug".) A report is one of:
+		        SuperlocusOutput      Report for superlocus classification.
+		        SuperlocusStats       Report for superlocus classification stats.
+		        LocusOutput           Report for locus classification.
+		        LocusStats            Report for locus stats.
+		        VariantOutput         Both variant files annotated by comparison 
+		                              results.If the somatic output report is 
+		                              requested, file A is also annotated with the 
+		                              same score ranks as produced in that report.
+		        SomaticOutput         Report for the list of simple variations that
+		                              are present only in file "A", annotated with 
+		                              the score that indicates the probability of 
+		                              the variation being truly somatic. Requires 
+		                              beta, genome-rootA, and genome-rootB options 
+		                              to be provided as well. Note: generating this
+		                              report slows calldiff by 10x-20x.
+		        DebugCallOutput       Report for call classification.
+		        DebugSuperlocusOutput Report for debug superlocus information.
+		        DebugSomaticOutput    Report for distribution estimates used for 
+		                              somatic rescoring. Only produced if 
+		                              SomaticOutput is also turned on.
+		
+		  --diploid 
+		      Uses varScoreEAF instead of varScoreVAF in somatic score computations. 
+		      Also, uses diploid variant model instead of variable allele mixture 
+		      model.
+		
+		  --locus-stats-column-count arg (=15)
+		      The number of columns for locus compare classification in the locus 
+		      stats file.
+		
+		  --max-hypothesis-count arg (=32)
+		      The maximum number of possible phasings to consider for a superlocus.
+		
+		  --no-reference-cover-validation 
+		      Turns off validation that all bases of a chromosome are covered by 
+		      calls of the variant file.
+		
+		  --genome-rootA arg
+		      The "A" genome directory, for example /data/GS00118-DNA_A01; this 
+		      directory is expected to contain ASM/REF and ASM/EVIDENCE 
+		      subdirectories.
+		
+		  --genome-rootB arg
+		      The "B" genome directory.
+		
+		  --calibration-root arg
+		      The directory containing calibration data. For example, there should 
+		      exist a file calibration-root/0.0.0/metrics.tsv.
+		
+		  --beta 
+		      This flag enables the SomaticOutput report, which is beta 
+		      functionality.
+		
+		SUPPORTED FORMAT_VERSION
+		  0.3 or later
+  </help>
+</tool>