changeset 16:0260ca585cef draft

Deleted selected files

--- a/AddOrReplaceReadGroups.xml	Tue Feb 04 13:16:26 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,241 +0,0 @@
-<tool name="Add or Replace Groups" id="picard_ARRG" version="1.99">
-  <command interpreter="java -jar -Xmx8g">
-      AddOrReplaceReadGroups.jar
-      INPUT="${inputFile}"
-      RGLB="${rglb}"
-      RGPL="${rgpl}"
-      RGPU="${rgpu}"
-      RGSM="${rgsm}"
-      RGID="${rgid}"
-      #if $readGroupOpts.rgOpts == "full"
-        RGCN="${readGroupOpts.rgcn}"
-        RGDS="${readGroupOpts.rgds}"
-        RGPI="${readGroupOpts.rgpi}"
-      #end if
-      #if $reporting.opt == "full"
-        VALIDATION_STRINGENCY="${reporting.vs}"
-        QUIET="${reporting.verbosity}"
-      #else
-        VALIDATION_STRINGENCY=LENIENT
-        QUIET=True
-      #end if        
-      OUTPUT="${outFile}"
-      TMP_DIR="${__new_file_path__}" 
-  </command>
-  
-  <stdio>
-    <exit_code range="0" level="warning" description="Tool finished correctly" />
-  </stdio>
-  
-  
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"
-      help="If empty, upload or import a SAM/BAM dataset." />
-    <param name="rgid" value="1" type="text" label="Read group ID (ID tag)" help="The most important read group tag. Galaxy will use a value of '1' if nothing provided." />
-    <param name="rgsm" value="" type="text" label="Read group sample name (SM tag)" />
-    <param name="rglb" value="" type="text" label="Read group library (LB tag)" />
-    <param name="rgpl" value="" type="text" label="Read group platform (PL tag)" help="illumina, solid, 454, pacbio, helicos" />
-    <param name="rgpu" value="" type="text" label="Read group platform unit" help="like run barcode, etc." />
-    <conditional name="readGroupOpts">
-      <param name="rgOpts" type="select" label="Specify additional (optional) arguments" help="Allows you to set GCN, RGDS, and RGPI">
-        <option value="preSet">Use pre-set defaults</option>
-        <option value="full">Set optional arguments</option>
-      </param>
-      <when value="preSet" />
-      <when value="full">
-        <param name="rgcn" value="" type="text" label="Read group sequencing center name" help="Leave set to &lt;null&gt; for default (none)" />
-        <param name="rgds" value="" type="text" label="Read group description" help="Leave set to &lt;null&gt; for default (none)" />
-        <param name="rgpi" value="" type="text" label="Predicted insert size" help="Leave set to &lt;null&gt; for default (none)" />
-      </when>
-    </conditional>
-    
-    <conditional name="reporting">
-      <param name="opt" type="select" label="Change reporting options" help="Allows you to set Validation Stringency and Verbosity">
-        <option value="preSet">Use pre-set defaults</option>
-        <option value="full">Set optional arguments</option>
-      </param>
-      <when value="preSet" />
-      <when value="full">
-        <param name="vs" type="select" label="Set validation stringency">
-            <option value="LENIENT" selected="True">Lenient</option>
-            <option value="STRICT">Strict</option>
-            <option value="SILENT">Silent</option>
-        </param>
-        <param name="verbosity" type="select" label="Enable or supress reporting of job summary to Standard Error">
-            <option value="True" selected="True">Supress</option>
-            <option value="False">Enable</option>
-        </param>
-       </when>
-    </conditional>
-    
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam">
-    </data>
-  </outputs>
-  <tests>
-  <test>
-      <!-- Command for replacing read groups in bam:
-      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT INPUT=./test-data/in-noHeader.sam OUTPUT=./test-data/PICARD-ARRG-test1.bam RGLB=test1 RGPL=Illumina RGPU=PLAT RGSM=sample1 RGID=test1 QUIET=True
-     -->
-      <param name="inputFile" value="PICARD-in-noHeader.sam" />
-      <param name="rglb" value="test1" />
-      <param name="rgpl" value="Illumina" />
-      <param name="rgpu" value="PLAT" />
-      <param name="rgsm" value="sample1" />
-      <param name="rgid" value="test1" />
-      <param name="rgOpts" value="preSet" />
-      <param name="opt" value="preSet" />
-      <output name="outFile" file="PICARD-ARRG-test1.bam" lines_diff="2" ftype="bam" />
-    </test>
-    <test>
-      <!-- Command for replacing read groups in sam:
-      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT INPUT=./test-data/in.sam OUTPUT=./test-data/PICARD-ARRG-test2.bam RGLB=test2 RGPL=Illumina RGPU=PLAT RGSM=sample2 RGID=test2 QUIET=True
-      picard_ARRG_input1.bam can be created from picard_ARRG_input1.sam
-      -->
-      <param name="inputFile" value="PICARD-in.sam" />
-      <param name="rglb" value="test2" />
-      <param name="rgpl" value="Illumina" />
-      <param name="rgpu" value="PLAT" />
-      <param name="rgsm" value="sample2" />
-      <param name="rgid" value="test2" />
-      <param name="rgOpts" value="preSet" />
-      <param name="opt" value="preSet" />
-      <output name="outFile" file="PICARD-ARRG-test2.bam" lines_diff="2" ftype="bam" />
-    </test>
-    <test>
-      <!-- Command for adding read groups in sam:
-      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT INPUT=./test-data/in.bam OUTPUT=./test-data/PICARD-ARRG-test3.bam RGLB=test3 RGPL=Illumina RGPU=PLAT RGSM=sample3 RGID=test3 QUIET=True
-      -->
-      <param name="inputFile" value="PICARD-in.bam" />
-      <param name="rglb" value="test3" />
-      <param name="rgpl" value="Illumina" />
-      <param name="rgpu" value="PLAT" />
-      <param name="rgsm" value="sample3" />
-      <param name="rgid" value="test3" />
-      <param name="rgOpts" value="preSet" />
-      <param name="opt" value="preSet" />
-      <output name="outFile" file="PICARD-ARRG-test3.bam" lines_diff="2" ftype="bam" />
-    </test>
-  </tests>
-  <help>
-
-.. class:: infomark
-
-**Purpose**
-
-Add or Replace Read Groups in an input BAM or SAM file.
-
-**Read Groups are Important!**
-
-Setting read groups correctly from the start will simplify your life greatly because you can merge multiple BAM files into one significantly reducing the number of analysis steps. Below we provide an explanation of read groups fields taken from GATK FAQ webpage:
-
-.. csv-table::
-   :header-rows: 1
-    
-    Tag,Importance,Definition,Meaning
-    "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number.  Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came.  Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
-    "SM","Sample. Use pool name where a pool is being sequenced.","Required.  As important as ID.","The name of the sample sequenced in this read group.  GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample.  Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
-    "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important.  Not currently used in the GATK, but was in the past, and may return.  The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field."
-    "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."
-
-**Example of Read Group usage**
-
-Support we have a trio of samples: MOM, DAD, and KID.  Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts.  Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data.  When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::
-
- Dad's data:
- @RG     ID:FLOWCELL1.LANE1      PL:illumina     LB:LIB-DAD-1 SM:DAD      PI:200
- @RG     ID:FLOWCELL1.LANE2      PL:illumina     LB:LIB-DAD-1 SM:DAD      PI:200
- @RG     ID:FLOWCELL1.LANE3      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
- @RG     ID:FLOWCELL1.LANE4      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
-  
- Mom's data:
- @RG     ID:FLOWCELL1.LANE5      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
- @RG     ID:FLOWCELL1.LANE6      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
- @RG     ID:FLOWCELL1.LANE7      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
- @RG     ID:FLOWCELL1.LANE8      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
- 
- Kid's data:
- @RG     ID:FLOWCELL2.LANE1      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
- @RG     ID:FLOWCELL2.LANE2      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
- @RG     ID:FLOWCELL2.LANE3      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
- @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
-
-Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
-
-**Picard documentation**
-
-This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: infomark
-
-**Inputs, outputs, and parameters**
-
-Either a sam file or a bam file must be supplied. If a bam file is used, it must
-be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
-
-The output file is either bam (the default) or sam, according to user selection,
-and contains the same information as the input file except for the appropraite
-additional (or modified) read group tags. Bam is recommended since it is smaller.
-
-From the Picard documentation.
-
-AddOrReplaceReadGroups REQUIRED parameters::
-
-  Option (Type)    Description
-  
-  RGLB=String      Read Group Library
-  RGPL=String      Read Group platform (e.g. illumina, solid)
-  RGPU=String      Read Group platform unit (eg. run barcode)
-  RGSM=String      Read Group sample name
-  RGID=String      Read Group ID; Default value: null (empty)
-
-AddOrReplaceReadGroups OPTIONAL parameters::
-
-  Option (Type)    Description
-  
-  RGCN=String      Read Group sequencing center name; Default value: null (empty)
-  RGDS=String      Read Group description Default value: null (empty)
-  
-AddOrReplaceReadGroups REPORTING parameters::
-
-  Option (Type)                                 Description
-  
-  VALIDATION_STRINGENCY=ValidationStringency    Validation stringency for all SAM files read by this program. 
-                                                Setting stringency to SILENT can improve performance when 
-                                                processing a BAM file in which variable-length data (read, 
-                                                qualities, tags) do not otherwise need to be decoded. 
-                                                Default value (in Galaxy): LENIENT. 
-                                                
-  QUIET=Boolean                                 Whether to suppress job-summary info on System.err. 
-                                                Default value (in Galaxy): True. 
-
-
-.. class:: warningmark
-
-**Warning on SAM/BAM quality**
-
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
-
-
-
-  </help>
-</tool>
-
-
-
-
-
-
-
-
-
-
-
-

--- a/picard_MergeBamAlignment.xml	Tue Feb 04 13:16:26 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,201 +0,0 @@
-<tool id="picard_mergeBAMAlignment" name="Merge BAM Alignment" version="1.106.0">
-    <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#MergeBamAlignment
-Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file and produces a third SAM or BAM file of aligned and unaligned reads. NOTE that this program expects to find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it to have the same base name as the reference fasta except with the extension '.dict'
-
-OUTPUT=File	Merged SAM or BAM file to write to. Required.
-REFERENCE_SEQUENCE=File	Path to the fasta file for the reference sequence. Required. 
--->
-  <description>Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file</description>
-  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="bash">
-     mergebamalignment_wrapper.sh $output1 $outformat $REFERENCE_SEQUENCE UNMAPPED_BAM=$UNMAPPED_BAM PAIRED_RUN=$PAIRED_RUN
-
-     ## optional arguments from here
-
-     #if str( $ALIGNED_BAM ):
-     ALIGNED_BAM=$ALIGNED_BAM
-     #end if
-     #for $i in $ALIGNED_BAMs
-       ALIGNED_BAM=${i.ALIGNED_BAM_file}
-     #end for 
-
-     #if str( $READ1_ALIGNED_BAM ):
-     READ1_ALIGNED_BAM=$READ1_ALIGNED_BAM
-     #end if
-     #for $i in $READ1_ALIGNED_BAMs
-       READ1_ALIGNED_BAM=${i.READ1_ALIGNED_BAM_file}
-     #end for 
-
-     #if str( $ATTRIBUTES_TO_RETAIN ):
-     ATTRIBUTES_TO_RETAIN=$ATTRIBUTES_TO_RETAIN
-     #end if
-     #for $i in $ATTRIBUTES_TO_RETAINs
-       ATTRIBUTES_TO_RETAIN=${i.ATTRIBUTES_TO_RETAIN_extra}
-     #end for 
-
-     #if str( $READ2_ALIGNED_BAM ):
-     READ2_ALIGNED_BAM=$READ2_ALIGNED_BAM
-     #end if
-     #for $i in $READ2_ALIGNED_BAMs
-       READ2_ALIGNED_BAM=${i.READ2_ALIGNED_BAM_file}
-     #end for 
-
-     #if str( $PROGRAM_RECORD_ID ):
-     PROGRAM_RECORD_ID=$PROGRAM_RECORD_ID
-     #end if
-
-     #if str( $PROGRAM_GROUP_VERSION ):
-     PROGRAM_GROUP_VERSION=$PROGRAM_GROUP_VERSION
-     #end if
-
-     #if str( $PROGRAM_GROUP_COMMAND_LINE ):
-     PROGRAM_GROUP_COMMAND_LINE=$PROGRAM_GROUP_COMMAND_LINE
-     #end if
-
-     #if str( $PROGRAM_GROUP_NAME ):
-     PROGRAM_GROUP_NAME=$PROGRAM_GROUP_NAME
-     #end if
-
-     #if str( $CLIP_ADAPTERS ):
-     CLIP_ADAPTERS=$CLIP_ADAPTERS
-     #end if
-
-     #if str( $IS_BISULFITE_SEQUENCE ):
-     IS_BISULFITE_SEQUENCE=$IS_BISULFITE_SEQUENCE
-     #end if
-
-     #if str( $ALIGNED_READS_ONLY ):
-     ALIGNED_READS_ONLY=$ALIGNED_READS_ONLY
-     #end if
-
-     #if str( $MAX_INSERTIONS_OR_DELETIONS ):
-     MAX_INSERTIONS_OR_DELETIONS=$MAX_INSERTIONS_OR_DELETIONS
-     #end if
-
-     #if str( $READ1_TRIM ):
-     READ1_TRIM=$READ1_TRIM
-     #end if
-
-     #if str( $READ2_TRIM ):
-     READ2_TRIM=$READ2_TRIM
-     #end if
-
-     #if str( $EXPECTED_ORIENTATIONS ):
-     EXPECTED_ORIENTATIONS=$EXPECTED_ORIENTATIONS
-     #end if
-
-     #if str( $SORT_ORDER ):
-     SORT_ORDER=$SORT_ORDER
-     #end if
-
-     #if str( $PRIMARY_ALIGNMENT_STRATEGY ):
-     PRIMARY_ALIGNMENT_STRATEGY=$PRIMARY_ALIGNMENT_STRATEGY
-     #end if
-
-     #if str( $CLIP_OVERLAPPING_READS ):
-     CLIP_OVERLAPPING_READS=$CLIP_OVERLAPPING_READS
-     #end if
-
-     #if str( $INCLUDE_SECONDARY_ALIGNMENTS ):
-     INCLUDE_SECONDARY_ALIGNMENTS=$INCLUDE_SECONDARY_ALIGNMENTS
-     #end if
-
-      VALIDATION_STRINGENCY=LENIENT TMP_DIR=$__new_file_path__
-          2&gt; $outlog
-    ##|| echo "Error running Picard MergeBamAlignment" >&amp;2
-  </command>
-  <inputs>
-<!-- required arguments below -->
-    <param name="title" label="Name for the output merged BAM or SAM file" type="text" default="Merged.bam" help="This name will appear in your history so use it to remember what the new file in your history contains" />
-    <param name="outformat" type="select" label="Output format" >
-      <option value="bam" selected="True">BAM</option>
-      <option value="sam">SAM</option>
-    </param>
-    <param name="UNMAPPED_BAM" label="Original SAM or BAM file of unmapped reads, which must be in queryname order.  Required." type="data" format="bam,sam" />
-    <param name="REFERENCE_SEQUENCE" label="Path to the fasta file for the reference sequence. Required." type="data" format="fasta" />
-    <param name="PAIRED_RUN" value="true" type="boolean"  label="Whether this is a paired-end run.   Required." truevalue="true" falsevalue="false" checked="yes" />
-
-<!-- optional arguments below -->
-
-    <param name="ALIGNED_BAM" label="SAM or BAM file(s) with alignment data.  This option may be specified 0 or more times. Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) READ2_ALIGNED_BAM (R2_ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
-    <repeat name="ALIGNED_BAMs" title="More ALIGNED_BAMs">
-      <param name="ALIGNED_BAM_file" label="ALIGNED_BAM" type="data" format="bam,sam" />
-    </repeat>
-    <param name="READ1_ALIGNED_BAM" label="SAM or BAM file(s) with alignment data from the first read of a pair.  This option may be specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM (ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
-    <repeat name="READ1_ALIGNED_BAMs" title="More READ1_ALIGNED_BAMs">
-      <param name="READ1_ALIGNED_BAM_file" label="READ1_ALIGNED_BAM" type="data" format="bam,sam" />
-    </repeat>
-    <param name="READ2_ALIGNED_BAM" label="SAM or BAM file(s) with alignment data from the second read of a pair.  This option may be specified 0 or more times.  Cannot be used in conjuction with option(s) ALIGNED_BAM (ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
-    <repeat name="READ2_ALIGNED_BAMs" title="More READ2_ALIGNED_BAMs">
-      <param name="READ2_ALIGNED_BAM_file" label="READ2_ALIGNED_BAM" type="data" format="bam,sam" />
-    </repeat>
-
-    <param name="PROGRAM_RECORD_ID" label="The program group ID of the aligner (if not supplied by the aligned file)." type="text" default=""
-    <param name="PROGRAM_GROUP_VERSION" label="The version of the program group (if not supplied by the aligned file)." type="text" default="">
-    <param name="PROGRAM_GROUP_COMMAND_LINE" label="The command line of the program group (if not supplied by the aligned file)." type="text" default="">
-    <param name="PROGRAM_GROUP_NAME" label="The name of the program group (if not supplied by the aligned file)." type="text" default="">
-    <param name="CLIP_ADAPTERS" value="true" type="boolean"  label="Whether to clip adapters where identified.  Default value: true." truevalue="true" falsevalue="false" checked="yes" />
-    <param name="IS_BISULFITE_SEQUENCE" value="false" type="boolean"  label="Whether the lane is bisulfite sequence (used when caculating the NM tag)." truevalue="true" falsevalue="false" checked="yes" />
-    <param name="ALIGNED_READS_ONLY" value="false" type="boolean" label="Whether to output only aligned reads." truevalue="true" falsevalue="false" checked="yes" />
-    <param name="MAX_INSERTIONS_OR_DELETIONS" value="1" type="integer"
-      label="The maximum number of insertions or deletions permitted for an alignment to be included." 
-      help="Alignments with more than this many insertions or deletions will be ignored.  Set to -1 to allow any number of insertions or deletions.  Default value: 1." />
-
-    <param name="ATTRIBUTES_TO_RETAIN" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging.  This option may be specified 0 or more times." type="text" default="">
-    <repeat name="ATTRIBUTES_TO_RETAINs" title="More ATTRIBUTES_TO_RETAIN">
-      <param name="ATTRIBUTES_TO_RETAIN_extra" label="ATTRIBUTES_TO_RETAIN" type="text" default="" />
-    </repeat>
-    <param name="READ1_TRIM" value="0" type="integer" label="The number of bases trimmed from the beginning of read 1 prior to alignment"/>
-    <param name="READ2_TRIM" value="0" type="integer" label="The number of bases trimmed from the beginning of read 2 prior to alignment"/>
-    <param name="EXPECTED_ORIENTATIONS" label="The name of the program group (if not supplied by the aligned file)." type="select">
-      <option value="null" selected="True">null</option>
-      <option value="FR">FR</option>
-      <option value="RF">RF</option>
-      <option value="TANDEM">TANDEM</option>
-    </param>
-    <param name="SORT_ORDER" label="The order in which the merged reads should be output.  Default value: coordinate." type="select">
-      <option value="coordinate" selected="True">coordinate</option>
-      <option value="queryname">queryname</option>
-      <option value="unsorted">unsorted</option>
-    </param>
-    <param name="PRIMARY_ALIGNMENT_STRATEGY" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragment, and none are marked as primary, more than one is marked as primary, or the primary alignment is filtered out for some reason." type="select" help="BestMapq expects that multiple alignments will be correlated with HI tag, and prefers the pair of 
-                              alignments with the largest MAPQ, in the absence of a primary selected by the aligner. EarliestFragment prefers the alignment which maps the earliest base in the read. Note that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for cases in which the aligner is not pair-aware, and does not output the HI tag. It simply picks the alignment for each end with the highest MAPQ, and makes those alignments primary, regardless of whether the two alignments make sense together.MostDistant is also for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. If all alignments would be chimeric, it picks the alignments for each end with the best MAPQ.  For all algorithms, ties are resolved arbitrarily.  Default value: BestMapq.">
-      <option value="BestMapq" selected="True">BestMapq</option>
-      <option value="EarliestFragment">EarliestFragment</option>
-      <option value="BestEndMapq">BestEndMapq</option>
-      <option value="MostDistant">MostDistant</option>
-    </param>
-
-    <param name="CLIP_OVERLAPPING_READS" value="true" type="boolean" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate." truevalue="true" falsevalue="false" checked="yes" />
-    <param name="INCLUDE_SECONDARY_ALIGNMENTS" value="true" type="boolean" label="If false, do not write secondary alignments to output." truevalue="true" falsevalue="false" checked="yes" />
-  </inputs>
-
-  <outputs>
-    <data format="bam" name="output1" label="${title}.${outformat}" >
-       <change_format>
-           <when input="outformat" value="sam" format="sam" />
-       </change_format>
-    </data>
-  </outputs>
-  <tests>
-	<!-- note: this test is untested :) -->
-      <test>
-          <param name="REFERENCE_SEQUENCE" value="merger.fasta" />
-          <param name="UNMAPPED_BAM" value="unmapped.sam" />
-          <param name="PAIRED_RUN" value="false" />
-          <param name="outformat" value="sam" />
-          <output name="output1" file="output_mergebamalignment" lines_diff="1"/> 
-      </test>
-  </tests>
-  <help>
-
-**What it does**
-
-Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file and produces a third SAM or BAM file of aligned and unaligned reads. NOTE that this program expects to find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it to have the same base name as the reference fasta except with the extension '.dict' 
-metadata such as read groups
- 
-.. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeBamAlignment
-
-
-  </help>
-</tool>