Mercurial > repos > fcaramia > contra

--- a/Contra/scripts/contra.xml	Sun Dec 02 19:48:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,286 +0,0 @@
-<tool id="contra_tool" name="Contra Copy number analysis" version="1.0.0">
-  <description>: Copy Number Analysis for Targeted Resequencing</description>
-  <requirements>
-    <requirement type="package" version="2.17.0">bedtools</requirement>
-  </requirements>
-  <command interpreter="perl">
-
-	contra_wrapper.pl
-
-	##Ref Genome
-	#if $genomeSource.refGenomeSource == "history":
-        	"PLAYEROPTION::-f=${genomeSource.ownFile}"
-        #else:
-        ##use precomputed indexes
-        	"PLAYEROPTION::-f=${genomeSource.indices.fields.path}"
-	#end if
-
-	##Required files
-	"PLAYEROPTION::-t=$target_file"
-	"PLAYEROPTION::-s=$alignment_file"
-	#if $controlSource.refControlSource == "history":
-         	"PLAYEROPTION::-c=${controlSource.control_file}"
-        #else:
-        ##use precomputed indexes
-        	"PLAYEROPTION::-c=${controlSource.indices.fields.path}"
-        #end if
-
-	##Optional parameter
-
-        #if $option.option == "modify_parameters":
-
-        	"PLAYEROPTION::--numBin=$option.numBin"
-        	"PLAYEROPTION::--minReadDepth=$option.minReadDepth"
-        	"PLAYEROPTION::--minNBases=$option.minNbases"
-
-		#if str($option.sam) == "true":
-	        	"PLAYEROPTION::--sam"
-        	#end if
-
-        	#if str($option.bed) == "true":
-	        	"PLAYEROPTION::--bed"
-        	#end if
-
-        	"PLAYEROPTION::--pval=$option.pval"
-        	"PLAYEROPTION::--sampleName=$option.sampleName"
-
-		#if str($option.nomultimapped) == "true":
-	        	"PLAYEROPTION::--nomultimapped"
-        	#end if
-
-        	#if str($option.plot) == "true":
-	        	"PLAYEROPTION::--plot"
-        	#end if
-
-        	"PLAYEROPTION::--minExon=$option.minExon"
-        	"PLAYEROPTION::--minControlRdForCall=$option.minControlRdForCall"
-        	"PLAYEROPTION::--minTestRdForCall=$option.minTestRdForCall"
-        	"PLAYEROPTION::--minAvgForCall=$option.minAvgForCall"
-        	"PLAYEROPTION::--maxRegionSize=$option.maxRegionSize"
-        	"PLAYEROPTION::--targetRegionSize=$option.targetRegionSize"
-
-        	#if str($option.largedeletion) == "true":
-	        	"PLAYEROPTION::--largedeletion"
-        	#end if
-
-        	"PLAYEROPTION::--smallSegment=$option.smallSegment"
-        	"PLAYEROPTION::--targetRegionSize=$option.targetRegionSize"
-        	"PLAYEROPTION::--largeSegment=$option.largeSegment"
-        	"PLAYEROPTION::--lrCallStart=$option.lrCallStart"
-        	"PLAYEROPTION::--lrCallEnd=$option.lrCallEnd"
-        	"PLAYEROPTION::--passSize=$option.passSize"
-        #end if
-
-	##File to generate the bam list
-	CONTRAOUTPUT::$html_file
-	CONTRADIR::$html_file.files_path
-
-  </command>
-	<inputs>
-
-		<conditional name="genomeSource">
-			<param name="refGenomeSource" type="select" label="Will you select a reference from your history or use a built-in fasta file?">
-				<option value="indexed">Use a built-in index</option>
-				<option value="history">Use one from the history</option>
-			</param>
-			<when value="indexed">
-				<param name="indices" type="select" label="Select a reference genome">
-				  <options from_data_table="all_fasta">
-				    <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="fasta" label="Select a reference from history" />
-			</when>
-		</conditional>
-
-		<param name="target_file" type="data" format="bed" help="" optional="false" />
-		<param name="alignment_file" type="data" format="bam,sam" help="" optional="false" />
-
-
-		<conditional name="controlSource">
-			<param name="refControlSource" type="select" label="Will you select a reference from your history or use a built-in control file?">
-				<option value="indexed">Use a built-in control</option>
-				<option value="history">Use one from the history</option>
-			</param>
-			<when value="indexed">
-				<param name="indices" type="select" label="Select a baseline control">
-				  <options from_data_table="baseline_files">
-				    <filter type="sort_by" column="2" />
-				    <validator type="no_options" message="No files available" />
-				  </options>
-				</param>
-			</when>
-			<when value="history">
-				<param name="control_file" type="data" format="bam,sam,bed,tabular" help="" optional="false" />
-			</when>
-		</conditional>
-
-		<conditional name="option">
-			<param name="option" type="select" label="Optional Parameters" help="" optional="true">
-				<option value="default_parameters" selected="true">Default Parameters</option>
-				<option value="modify_parameters">Modify Parameters</option>
-			</param>
-			<when value="modify_parameters">
-				<param name="numBin"  type="integer" value="20" optional="true" />
-				<param name="minReadDepth"  type="integer" value="10" optional="true" />
-				<param name="minNbases"  type="integer" value="10" optional="true" />
-				<param name="sam" type="select" label="sam" help="" optional="true">
-					<option value="true"  >true</option>
-					<option value="false" selected="true">false</option>
-				</param>
-				<param name="bed" type="select" label="bed" help="" optional="true">
-					<option value="true"  >true</option>
-					<option value="false" selected="true">false</option>
-				</param>
-				<param name="pval"  type="float" value="0.05" optional="true" />
-				<param name="sampleName" value="Contra_Output" type="text"  optional="true" />
-				<param name="nomultimapped" type="select" label="no multimapped" help="" optional="true">
-					<option value="true"  >true</option>
-					<option value="false" selected="true">false</option>
-				</param>
-				<param name="plot" type="select" label="plot" help="" optional="true">
-					<option value="true"  >true</option>
-					<option value="false" selected="true">false</option>
-				</param>
-				<param name="minExon"  type="integer" value="2000" optional="true" />
-				<param name="minControlRdForCall"  type="integer" value="5" optional="true" />
-				<param name="minTestRdForCall"  type="integer" value="0" optional="true" />
-				<param name="minAvgForCall"  type="integer" value="20" optional="true" />
-				<param name="maxRegionSize"  type="integer" value="0" optional="true" />
-				<param name="targetRegionSize"  type="integer" value="200" optional="true" />
-				<param name="largedeletion" type="select" label="large deletion" help="" optional="true">
-					<option value="true"  >true</option>
-					<option value="false" selected="true">false</option>
-				</param>
-
-				<param name="smallSegment"  type="integer" value="1" optional="true" />
-				<param name="largeSegment"  type="integer" value="25" optional="true" />
-				<param name="lrCallStart"  type="float" value="-0.3" optional="true" />
-				<param name="lrCallEnd"  type="float" value="0.3" optional="true" />
-				<param name="passSize"  type="float" value="0.5" optional="true" />
-
-			</when>
-		</conditional>
-	</inputs>
-	<outputs>
-		<data name="html_file" format="html" label="Contra Output" />
-	</outputs>
-	<help>
-|
-
-
-**Reference**
-	http://contra-cnv.sourceforge.net/
-
------
-
-**What it does**
-
-CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package.
-
-
------
-
-**Required Parameters**
-
-::
-
-  -t, --target         Target region definition file [BED format]
-
-  -s, --test           Alignment file for the test sample [BAM/SAM]
-
-  -c, --control        Alignment file for the control sample
-                       [BAM/SAM/BED – baseline file]
-
-  --bed                **option has to be supplied for control
-                       with baseline file.**
-
-  -f, --fasta          Reference genome [FASTA]
-
-  -o, --outFolder      the folder name (and its path) to store the output
-                       of the analysis (this new folder will be created –
-                       error message occur if the folder exists)
-
------
-
-**Optional Parameters**
-
-::
-
-  --numBin              Numbers of bins to group the regions. User can
-                        specify multiple experiments with different numbers
-                        of bins (comma separated). [Default: 20]
-
-  --minReadDepth        The threshold for minimum read depth for each bases
-                        (see Step 2 in CONTRA workflow) [Default: 10]
-
-  --minNBases           The threshold for minimum number of bases for each
-                        target regions (see Step 2 in CONTRA workflow)
-                        [Default: 10]
-
-  --sam                 If the specified test and control samples are in
-                        SAM format. [Default: False] (It will always take
-                        BAM samples as default)
-
-  --bed                 If specified, control will be a baseline file in
-                        BED format. [Default: False]
-                        Please refer to the Baseline Script section for
-                        instruction how to create baseline files from set
-                        of BAMfiles. A set of baseline files from different
-                        platform have also been provided in the CONTRA
-                        download page.
-
-  --pval                The p-value threshold for filtering. Based on Adjusted
-                        P-Values. Only regions that pass this threshold will
-                        be included in the VCF file. [Default: 0.05]
-
-  --sampleName          The name to be appended to the front of the default output
-                        name. By default, there will be nothing appended.
-
-  --nomultimapped       The option to remove multi-mapped reads
-                        (using SAMtools with mapping quality > 0).
-                        [default: FALSE]
-
-  -p, --plot            If specified, plots of log-ratio distribution for each
-                        bin will be included in the output folder [default: FALSE]
-
-  --minExon             Minimum number of exons in one bin (if less than this number
-                        , bin that contains small number of exons will be merged to
-                        the adjacent bins) [Default : 2000]
-
-  --minControlRdForCall Minimum Control ReadDepth for call [Default: 5]
-
-  --minTestRdForCall    Minimum Test ReadDepth for call [Default: 0]
-
-  --minAvgForCall       Minimum average coverage for call [Default: 20]
-
-  --maxRegionSize       Maximum region size in target region (for breaking
-                        large regions into smaller regions. By default,
-                        maxRegionSize=0 means no breakdown). [Default : 0]
-
-  --targetRegionSize    Target region size for breakdown (if maxRegionSize
-                        is non-zero) [Default: 200]
-
-  -l, --largeDeletion   If specified, CONTRA will run large deletion analysis (CBS).
-                        User must have DNAcopy R-library installed to run the
-                        analysis. [False]
-
-  --smallSegment        CBS segment size for calling large variations [Default : 1]
-
-  --largeSegment        CBS segment size for calling large variations [Default : 25]
-
-  --lrCallStart         Log ratios start range that will be used to call CNV
-                        [Default : -0.3]
-
-  --lrCallEnd           Log ratios end range that will be used to call CNV
-                        [Default : 0.3]
-
-  --passSize            Size of exons that passed the p-value threshold compare
-                        to the original exons size [Default: 0.5]
-	</help>
-</tool>
-
-