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author dongjun
date Wed, 21 Sep 2011 03:27:06 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mosaics.xml	Wed Sep 21 03:27:06 2011 -0400
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+<tool id="MOSAiCS" name="MOSAiCS: MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data" version="1.0.0">
+  
+  <description></description>
+	
+  <parallelism method="basic"></parallelism>
+  
+  <requirements>
+	  <requirement type="binary">R</requirement>
+  </requirements>
+
+  <command interpreter="perl">
+    mosaics_wrapper.pl 
+      ## input file name (chip and control)
+      $chipParams.chip
+      $controlParams.control
+      ## input file format (chip and control)
+      $chipParams.chipFileFormat
+      $controlParams.controlFileFormat
+      ## peak file name
+      $out_peak
+      ## peak file format
+      $OutfileFormat
+      ## analysis type
+      IO
+      ## optional output
+      $report_summary
+      $report_gof
+      $report_exploratory
+      ## settings for model fitting and peak calling: required (0.05, 200, 50)
+      $fdrLevel
+      $fragLen
+      $binSize
+      $capping
+      ## settings for model fitting and peak calling: optional
+      #if $fitParams.fSettingsType == "preSet"
+	BIC
+	0.25
+	200
+	50
+	10
+      #else
+	$fitParams.signalModel
+	$fitParams.d
+	$fitParams.maxgap
+	$fitParams.minsize	
+	$fitParams.thres
+      #end if
+      ## Number of cores to use
+      8
+  </command>
+
+  <inputs>
+	<conditional name="chipParams">
+		<param name="chipFileFormat" type="select" label="Select file format for ChIP sample" help="MOSAiCS can accept aligned read files.">
+			<option value="eland_result">Eland result</option>
+			<option value="eland_extended">Eland extended</option>
+			<option value="eland_export">Eland export</option>
+			<option value="bowtie">Bowtie default</option>
+			<option value="sam">SAM</option>
+		</param>
+		<when value="eland_result">
+			<param name="chip" type="data" format="eland" label="Eland result file for ChIP sample"/>
+		</when>
+		<when value="eland_extended">
+			<param name="chip" type="data" format="eland" label="Eland extended file for ChIP sample"/>
+		</when>
+		<when value="eland_export">
+			<param name="chip" type="data" format="eland" label="Eland export file for ChIP sample"/>
+		</when>
+		<when value="bowtie">
+			<param name="chip" type="data" label="Bowtie default file for ChIP sample"/>
+		</when>
+		<when value="sam">
+			<param name="chip" type="data" format="sam" label="SAM file for ChIP sample"/>
+		</when>
+	</conditional> <!-- chipParams -->
+	<conditional name="controlParams">
+		<param name="controlFileFormat" type="select" label="Select file format for control sample" help="MOSAiCS can accept aligned read files.">
+			<option value="eland_result">Eland result</option>
+			<option value="eland_extended">Eland extended</option>
+			<option value="eland_export">Eland export</option>
+			<option value="bowtie">Bowtie default</option>
+			<option value="sam">SAM</option>
+		</param>
+		<when value="eland_result">
+			<param name="control" type="data" format="eland" label="Eland result file for control sample"/>
+		</when>
+		<when value="eland_extended">
+			<param name="control" type="data" format="eland" label="Eland extended file for control sample"/>
+		</when>
+		<when value="eland_export">
+			<param name="control" type="data" format="eland" label="Eland export file for control sample"/>
+		</when>
+		<when value="bowtie">
+			<param name="control" type="data" label="Bowtie default file for control sample"/>
+		</when>
+		<when value="sam">
+			<param name="control" type="data" format="sam" label="SAM file for control sample"/>
+		</when>
+	</conditional> <!-- inputParams -->
+	
+	<param name="OutfileFormat" type="select" label="Select file format for peak calling results" help="MOSAiCS can export peak calling results into BED or GFF file formats, or as a table.">
+		<option value="bed">BED</option>
+		<option value="gff">GFF</option>
+		<option value="txt">table</option>
+	</param>
+	<param name="summary" type="boolean" truevalue="1" falsevalue="0" display="checkboxes" label="Reports for diagnostics: Summary of model fitting and peak calling" />
+	<param name="gof" type="boolean" truevalue="1" falsevalue="0" display="checkboxes" label="Reports for diagnostics: Goodness of fit (GOF) plots" />
+	<param name="exploratory" type="boolean" truevalue="1" falsevalue="0" display="checkboxes" label="Reports for diagnostics: Plots of exploratory analysis" />
+	
+	<param name="fdrLevel" type="float" value="0.05" min="0" max="1" label="False discovery rate (FDR)" help="FDR level for peak detection (default: 0.05)" />
+	<param name="fragLen" type="integer" value="200" label="Average fragment length" help="Default: 200." />
+	<param name="binSize" type="integer" value="200" label="Bin size" help="By default, bin size equals to the average fragment length." />
+	<param name="capping" type="integer" value="3" label="Maximum number of reads allowed to start at each nucleotide position" help="Small value (e.g., 3) are recommended for the ChIP-seq data with low sequencing depth and large value (e.g., 10000) for the ChIP-seq data with high sequencing depth." />
+	
+	<conditional name="fitParams">
+		<param name="fSettingsType" type="select" label="Settings for model fitting and peak calling" help="For most peak calling applications, use the 'Commonly used' setting. If you want access to all parameters, use 'Full parameter list'.">
+			<option value="preSet">Commonly used</option>
+			<option value="full">Full parameter list</option>
+		</param>
+		<when value="preSet" />
+		<when value="full">
+			<param name="signalModel" type="select" label="Signal model" help="By default, signal model is chosen using BIC. Instead, user can specify signal model among one or two signal component models.">
+				<option value="BIC">Automatic model selection based on BIC</option>
+				<option value="1S">One-signal-component model</option>
+				<option value="2S">Two-signal-component model</option>
+			</param>
+			<param name="d" type="float" value="0.25" label="d" help="Parameter for estimating background distribution. Default is 0.25." />
+			<param name="maxgap" type="integer" value="200" label="maxgap" help="Initial nearby peaks are merged if the distance (in bp) between them is less than 'maxgap'. Default is 200." />
+			<param name="minsize" type="integer" value="50" label="minsize" help="An initial peak is removed if its width is narrower than 'minsize'. Default is 50." />
+			<param name="thres" type="integer" value="10" label="thres" help="A bin within initial peak is removed if its ChIP tag counts are less than 'thres'. Default is 10." />
+		</when> <!-- full -->
+	</conditional> <!-- fitParams -->
+  </inputs>
+
+  <outputs>
+	<data format="tabular" name="out_peak">
+		<change_format>
+			<when input="OutfileFormat" value="bed" format="bed" />
+			<when input="OutfileFormat" value="gff" format="gff" />
+		</change_format>
+	</data>
+	<data format="txt" name="report_summary">
+		<filter>summary == 1</filter>
+	</data>
+	<data format="pdf" name="report_gof">
+		<filter>gof == 1</filter>
+	</data>
+	<data format="pdf" name="report_exploratory">
+		<filter>exploratory == 1</filter>
+	</data>
+  </outputs>
+
+  <help>
+
+**What it does**
+
+MOSAiCS is a statistical framework for the analysis of ChIP-seq data and it stands for MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data. MOSAiCS is based on a flexible parametric mixture modeling approach for detecting peaks (i.e., enriched regions).
+MOSAiCS is also available in Bioconductor_ as a R package.
+We encourage questions or requests regarding MOSAiCS to be posted on our `Google group`_.
+
+Please cite: Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, and Keles S (2011), "`A statistical framework for the analysis of ChIP-Seq data`_," To appear in the *Journal of the American Statistical Association*.
+
+.. _Bioconductor: http://www.bioconductor.org/help/bioc-views/2.8/bioc/html/mosaics.html
+.. _Google group: http://groups.google.com/group/mosaics_user_group
+.. _A statistical framework for the analysis of ChIP-Seq data: http://pubs.amstat.org/doi/abs/10.1198/jasa.2011.ap09706
+
+------
+
+**Input formats**
+
+MOSAiCS accepts aligned read files of ChIP and control samples as input. Currently, MOSAiCS accepts single-end reads, in Eland result, Eland extended, Eland export, Bowtie default, and SAM formats.
+
+------
+
+**Outputs**
+
+Peak calling results of MOSAiCS can be exported into BED or GFF file formats, or as a table. Each line of the output file specifies a single peak.
+
+If the output is a table, it has the following columns::
+
+   Column    Description
+   --------  --------------------------------------------------------
+     1       Chromosome of the peak
+     2       Start position of the peak
+     3       End position of the peak
+     4       Width of the peak
+     5       Averaged posterior probability of the peak
+     6       Minimum posterior probability of the peak
+     7       Averaged ChIP tag counts of the peak
+     8       Maximum ChIP tag counts of the peak
+     9       Averaged control tag counts of the peak
+    10       Averaged control tag counts of the peak, scaled by sequencing depth
+    11       Averaged log base 2 ratio of ChIP over input tag counts
+
+If the output is in BED format, it has the following columns::
+
+    Column        Description
+    ------------  --------------------------------------------------------
+    1 chrom       Chromosome of the peak
+    2 chromStart  Start position of the peak
+    3 chromEnd    End position of the peak
+    4 name        Always "MOSAiCS_peak"
+    5 score       Averaged ChIP tag counts of the peak
+
+If the output is in GFF format, it has the following columns::
+
+    Column     Description
+    ---------  --------------------------------------------------------
+    1 seqname  Chromosome of the peak
+    2 source   Always "MOSAiCS"
+    3 feature  Always "MOSAiCS_peak"
+    4 start    Start position of the peak
+    5 end      End position of the peak
+    6 score    Averaged ChIP tag counts of the peak
+    7 strand   Always "."
+    8 frame    Always "."
+    9 group    Always "."
+
+------
+
+**Reports for diagnostics**
+
+*Summary of model fitting and peak calling*: This report provides information about input and output files, parameter settings used for model fitting and peak calling, and brief summary of peak calling results. 
+
+*Goodness of fit (GOF) plots*: This report allows visual comparisons of the fits of the background, one-signal-component, and two-signal-component models with the actual data. 
+
+*Plots of exploratory analysis*: This report provides the histograms of ChIP and control samples and the scatter plots of ChIP versus control tag counts.
+
+More details regarding these reports can be found here_:
+
+------
+
+**Settings for model fitting and peak calling**
+
+More details about the tuning of these parameters can be found here_:
+
+.. _here: http://www.bioconductor.org/packages/2.8/bioc/vignettes/mosaics/inst/doc/mosaics-example.pdf
+
+  </help>
+</tool>