Mercurial > repos > fcaramia > contra
diff Contra/contra.xml @ 8:1a5cbabc4cd3
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| author | fcaramia |
|---|---|
| date | Sun, 02 Dec 2012 19:48:13 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Contra/contra.xml Sun Dec 02 19:48:13 2012 -0500 @@ -0,0 +1,286 @@ +<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> + +