--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_EstimateLibraryComplexity.xml	Mon Jul 06 14:46:32 2015 -0400
@@ -0,0 +1,132 @@
+<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="1.135">
+  <description>assess sequence library complexity from read sequences</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>
+    @java_options@
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    EstimateLibraryComplexity
+    
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    
+    MIN_IDENTICAL_BASES="${min_identical_bases}"
+    MAX_DIFF_RATE="${max_diff_rate}"
+    MIN_MEAN_QUALITY="${min_mean_quality}"
+    MAX_GROUP_RATIO="${max_group_ratio}"
+    #import pipes
+    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
+    
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
+    <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
+    <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
+    <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>
+    <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>
+
+    <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
+      <sanitizer>
+        <valid initial="string.printable">
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
+
+   <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/>
+      <param name="min_identical_bases" value="5"/>
+      <param name="max_diff_rate" value="0.03"/>
+      <param name="min_mean_quality" value="20"/>
+      <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
+      <param name="optical_duplicate_pixel_distance" value="100"/>
+      <param name="max_group_ratio" value="500"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Attempts to estimate library complexity from sequence of read pairs alone. Does so by sorting all reads by the first N bases (5 by default)
+of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates
+if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).
+
+Reads of poor quality are filtered out so as to provide a more accurate estimate. The filtering removes reads with any no-calls in the first
+N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read.
+
+Unpaired reads are ignored in this computation.
+The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size.
+
+Also, since there is no alignment to screen out technical reads one further filter is applied on the data. After examining all reads a Histogram
+is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram
+as outliers before library size is estimated.
+
+@dataset_collections@
+
+@description@
+
+  MIN_IDENTICAL_BASES=Integer   The minimum number of bases at the starts of reads that must be identical for reads to be 
+                                grouped together for duplicate detection.  In effect total_reads / 4^max_id_bases reads 
+                                will be compared at a time, so lower numbers will produce more accurate results but 
+                                consume exponentially more memory and CPU.  Default value: 5. 
+  
+  MAX_DIFF_RATE=Double          The maximum rate of differences between two reads to call them identical.  Default value: 
+                                0.03.
+  
+  MIN_MEAN_QUALITY=Integer      The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads 
+                                with lower average quality are filtered out and not considered in any calculations.  
+                                Default value: 20.
+  
+  MAX_GROUP_RATIO=Integer       Do not process self-similar groups that are this many times over the mean expected group 
+                                size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then 
+                                the mean expected group size would be approximately 10 reads.  Default value: 500.
+  
+  READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read 
+                                names are parsed to extract three variables: tile/region, x coordinate and y coordinate. 
+                                These values are used to estimate the rate of optical duplication in order to give a more 
+                                accurate estimated library size. Set this option to null to disable optical duplicate 
+                                detection. The regular expression should contain three capture groups for the three 
+                                variables, in order. It must match the entire read name. Note that if the default regex 
+                                is specified, a regex match is not actually done, but instead the read name  is split on 
+                                colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be 
+                                tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements 
+                                are assumed to be tile, x and y values.  Default value: 
+                                [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
+  
+  OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer  
+                                The maximum offset between two duplicte clusters in order to consider them optical 
+                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) 
+                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in 
+                                which case 50-100 is more normal.  Default value: 100.
+  
+
+@more_info@
+
+  </help>
+</tool>
+
+