--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Mon Jul 06 14:46:32 2015 -0400
@@ -0,0 +1,160 @@
+<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="1.135">
+  <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>
+    @java_options@
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    MarkDuplicatesWithMateCigar
+    
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    
+    METRICS_FILE="${metrics_file}"
+    COMMENT="${comment}"
+
+    MINIMUM_DISTANCE="${minimum_distance}"
+    SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}"
+    
+    
+    REMOVE_DUPLICATES="${remove_duplicates}"
+    ASSUME_SORTED="${assume_sorted}"
+    
+    DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
+    
+    #import pipes
+    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
+    
+    
+    BLOCK_SIZE=100000
+    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="comment" type="text" size="50" label="Add this comment to BAM dataset"/>
+    
+    <param name="minimum_distance" type="integer" value="-1" label="The minimum distance to buffer records to account for clipping on the 5' end of the records" help="MINIMUM_DISTANCE; Set this number to -1 to use twice the first read's read length (or 100, whichever is smaller); default=-1"/>
+    <param name="skip_pairs_with_no_mate_cigar" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Skip record pairs with no mate cigar and include them in the output" help="SKIP_PAIRS_WITH_NO_MATE_CIGAR; default=True"/>
+    <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
+
+    <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=TOTAL_MAPPED_REFERENCE_LENGTH">
+      <option value="TOTAL_MAPPED_REFERENCE_LENGTH" select="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
+      <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
+    </param>
+
+
+    <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="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/>
+      <param name="minimum_distance" value="-1"/>
+      <param name="skip_pairs_with_no_mate_cigar" value="True"/>
+      <param name="comment" value="test-run"/>
+      <param name="assume_sorted" value="True"/>
+      <param name="remove_duplicates" value="False"/>
+      <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="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Examines aligned records in the supplied SAM or BAM dataset to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged.
+
+------
+
+.. class:: warningmark
+
+On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar**
+
+From Samtools Announce MailingList_:
+
+This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed
+(see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation).  This allows the new tool
+to perform a streaming duplicate marking routine (i.e. a single-pass).  This tool cannot be used with
+alignments that have large gaps or reference skips, which happens frequently in RNA-seq data.
+
+.. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/
+
+@dataset_collections@
+
+@description@
+
+  MINIMUM_DISTANCE=Integer      The minimum distance to buffer records to account for clipping on the 5' end of the 
+                                records.Set this number to -1 to use twice the first read's read length (or 100, 
+                                whichever is smaller).  Default value: -1. This option can be set to 'null' to clear the 
+                                default value. 
+  
+  SKIP_PAIRS_WITH_NO_MATE_CIGAR=Boolean
+                                Skip record pairs with no mate cigar and include them in the output.  Default value: 
+                                true. This option can be set to 'null' to clear the default value. Possible values: 
+                                {true, false} 
+
+  COMMENT=String  
+  CO=String                     Comment(s) to include in the output file's header.  This option may be specified 0 or 
+                                more times. 
+
+  REMOVE_DUPLICATES=Boolean     If true do not write duplicates to the output file instead of writing them with 
+                                appropriate flags set.  Default value: false.  
+  
+  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]+).*.
+                                
+  DUPLICATE_SCORING_STRATEGY=ScoringStrategy
+  DS=ScoringStrategy            The scoring strategy for choosing the non-duplicate among candidates.  Default value: 
+                                TOTAL_MAPPED_REFERENCE_LENGTH. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} 
+  
+  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>
+
+