# HG changeset patch
# User crs4
# Date 1395420975 14400
# Node ID ebb02ba5987c0a6577e5c899beca6cad93ea812c
# Parent  6820983ba5d5218f8df18105c1c9c78b44c98bb5
Rewrite of param handling. interPairEnd param moved to "paired" section. Add param for '-a' option. Remove basic parallelism tag, which does not work with multiple inputs (thanks Bjoern Gruening for the notice). Simplify Python code.

diff -r 6820983ba5d5 -r ebb02ba5987c bwa_mem.py
--- a/bwa_mem.py	Tue Mar 18 07:49:22 2014 -0400
+++ b/bwa_mem.py	Fri Mar 21 12:56:15 2014 -0400
@@ -18,25 +18,6 @@
 
 import optparse, os, shutil, subprocess, sys, tempfile
 
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def check_is_double_encoded( fastq ):
-    # check that first read is bases, not one base followed by numbers
-    bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ]
-    nums = [ '0', '1', '2', '3' ]
-    for line in file( fastq, 'rb'):
-        if not line.strip() or line.startswith( '@' ):
-            continue
-        if len( [ b for b in line.strip() if b in nums ] ) > 0:
-            return False
-        elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):
-            return True
-        else:
-            raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space'
-    raise Exception, 'There is no non-comment and non-blank line in your FASTQ file'
-
 def __main__():
     descr = "bwa_mem.py: Map (long length) reads against a reference genome with BWA-MEM."
     parser = optparse.OptionParser(description=descr)
@@ -50,20 +31,20 @@
     parser.add_option( '-s', '--fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
     parser.add_option( '-D', '--dbkey', help='Dbkey for reference genome' )
 
-    parser.add_option( '-k', '--minEditDistSeed', default=19, type=int, help='Minimum edit distance to the seed [19]' )
-    parser.add_option( '-w', '--bandWidth', default=100, type=int, help='Band width for banded alignment [100]' )
-    parser.add_option( '-d', '--offDiagonal', default=100, type=int, help='off-diagonal X-dropoff [100]' )
-    parser.add_option( '-r', '--internalSeeds', default=1.5, type=float, help='look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' )
-    parser.add_option( '-c', '--seedsOccurrence', default=10000, type=int, help='skip seeds with more than INT occurrences [10000]' )
-    parser.add_option( '-S', '--mateRescue', default=False, help='skip mate rescue' )
-    parser.add_option( '-P', '--skipPairing', default=False, help='skpe pairing, mate rescue performed unless -S also in use' )
-    parser.add_option( '-A', '--seqMatch', default=1, type=int, help='score of a sequence match' )
-    parser.add_option( '-B', '--mismatch', default=4, type=int, help='penalty for a mismatch' )
-    parser.add_option( '-O', '--gapOpen', default=6, type=int, help='gap open penalty' )
-    parser.add_option( '-E', '--gapExtension', default=None, help='gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]' )
-    parser.add_option( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' )
-    parser.add_option( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' )
-    parser.add_option( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' )
+    parser.add_option( '-k', '--minSeedLength', type=int, help='Minimum seed length [19]' )
+    parser.add_option( '-w', '--bandWidth', type=int, help='Band width for banded alignment [100]' )
+    parser.add_option( '-d', '--offDiagonal', type=int, help='Off-diagonal X-dropoff [100]' )
+    parser.add_option( '-r', '--internalSeeds', type=float, help='Look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' )
+    parser.add_option( '-c', '--seedsOccurrence', type=int, help='Skip seeds with more than INT occurrences [10000]' )
+    parser.add_option( '-S', '--mateRescue', action='store_true', help='Skip mate rescue' )
+    parser.add_option( '-P', '--skipPairing', action='store_true', help='Skip pairing' )
+    parser.add_option( '-A', '--seqMatch', type=int, help='Score for a sequence match [1]' )
+    parser.add_option( '-B', '--mismatch', type=int, help='Penalty for a mismatch [4]' )
+    parser.add_option( '-O', '--gapOpen', type=int, help='Gap open penalty [6]' )
+    parser.add_option( '-E', '--gapExtension', type=int, help='Gap extension penalty; a gap of length k costs {-O} + {-E}*k [1]' )
+    parser.add_option( '-L', '--clipping', help='Penalty for clipping [5]' )
+    parser.add_option( '-U', '--unpairedReadpair', type=int, help='Penalty for an unpaired read pair [17]' )
+    parser.add_option( '-p', '--interPairEnd', action='store_true', help='FASTQ file consists of interleaved paired-end sequences' )
     parser.add_option( '--rgid', help='Read group identifier' )
     parser.add_option( '--rgsm', help='Sample' )
     parser.add_option( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' )
@@ -76,9 +57,10 @@
     parser.add_option( '--rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' )
     parser.add_option( '--rgpg', help='Programs used for processing the read group' )
     parser.add_option( '--rgpi', help='Predicted median insert size' )
-    parser.add_option( '-T', '--minScore', default=30, type=int, help='minimum score to output [30]' )
-    parser.add_option( '-M', '--mark', default=False, help='mark shorter split hits as secondary (for Picard/GATK compatibility)' )
-    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    parser.add_option( '-T', '--minScore', type=int, help='Minimum score to output [30]' )
+    parser.add_option( '-a', '--outputAll', action='store_true', help='Output all found alignments for single-end or unpaired paired-end reads' )
+    parser.add_option( '-M', '--mark', action='store_true', help='Mark shorter split hits as secondary (for Picard/GATK compatibility)' )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', action='store_true', help='Suppress header' )
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
@@ -152,7 +134,7 @@
                 shutil.rmtree( tmp_index_dir )
             if os.path.exists( tmp_dir ):
                 shutil.rmtree( tmp_dir )
-            stop_err( 'Error indexing reference sequence. ' + str( e ) )
+            raise Exception, 'Error indexing reference sequence. ' + str( e )
     else:
         ref_file_name = options.ref
     # if options.illumina13qual:
@@ -161,29 +143,45 @@
     #     illumina_quals = ""
 
     # set up aligning and generate aligning command args
-    start_cmds = '-t %s ' % options.threads
-    if options.params == 'pre_set':
-        # aligning_cmds = '-t %s %s' % ( options.threads, illumina_quals )
-        #start_cmds = '-t %s ' % options.threads
-        end_cmds = ' '
-        print start_cmds, end_cmds
-
-    else:
-        end_cmds = '-k %s -w %s -d %s -r %s -c %s -A %s -B %s -O %s -L %s -U %s -T %s ' % (options.minEditDistSeed, options.bandWidth, options.offDiagonal, options.internalSeeds, options.seedsOccurrence, options.seqMatch, options.mismatch, options.gapOpen, options.clipping, options.unpairedReadpair, options.minScore)
+    start_cmds = "bwa mem -t %s" % options.threads
+    if options.interPairEnd:
+        start_cmds += ' -p'
+    if options.params != 'pre_set':
+        if options.minSeedLength is not None:
+            start_cmds += " -k %d" % options.minSeedLength
+        if options.bandWidth is not None:
+            start_cmds += " -w %d" % options.bandWidth
+        if options.offDiagonal is not None:
+            start_cmds += " -d %d" % options.offDiagonal
+        if options.internalSeeds is not None:
+            start_cmds += " -r %s" % options.internalSeeds
+        if options.seedsOccurrence is not None:
+            start_cmds += " -c %d" % options.seedsOccurrence
         if options.mateRescue:
-            end_cmds += '-S '
-            if options.skipPairing:
-                end_cmds += '-P '
-        else:
-            if options.skipPairing:
-                print "Option Error and will not be considered, you should also choose 'skip mate rescue -S' option! "
-        if options.gapExtension != None:
-            end_cmds += '-E %s ' % options.gapExtension
-
+            start_cmds += ' -S'
+        if options.skipPairing:
+            start_cmds += ' -P'
+        if options.seqMatch is not None:
+            start_cmds += " -A %d" % options.seqMatch
+        if options.mismatch is not None:
+            start_cmds += " -B %d" % options.mismatch
+        if options.gapOpen is not None:
+            start_cmds += " -O %d" % options.gapOpen
+        if options.gapExtension is not None:
+            start_cmds += " -E %d" % options.gapExtension
+        if options.clipping:
+            start_cmds += " -L %s" % options.clipping
+        if options.unpairedReadpair is not None:
+            start_cmds += " -U %d" % options.unpairedReadpair
+        if options.minScore is not None:
+            start_cmds += " -T %d" % options.minScore
+        if options.outputAll:
+            start_cmds += ' -a'
+        if options.mark:
+            start_cmds += ' -M'
         if options.rgid:
             if not options.rglb or not options.rgpl or not options.rgsm or not options.rglb:
-                stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
-            # readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
+                sys.exit( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
             readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
             if options.rgpu:
                 readGroup += '\tPU:%s' % options.rgpu
@@ -201,67 +199,58 @@
                 readGroup += '\tPG:%s' % options.rgpg
             if options.rgpi:
                 readGroup += '\tPI:%s' % options.rgpi
-            end_cmds += ' -R "%s" ' % readGroup
-
-        if options.interPairEnd:
-            end_cmds += '-p %s ' % options.interPairEnd
-        if options.mark:
-            end_cmds += '-M '
-
+            start_cmds += " -R '%s'" % readGroup
 
     if options.genAlignType == 'paired':
-        cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, options.output )
+        cmd = "%s %s %s %s > %s" % ( start_cmds, ref_file_name, fastq, rfastq, options.output )
     else:
-        cmd = 'bwa mem %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, options.output )
+        cmd = "%s %s %s > %s" % ( start_cmds, ref_file_name, fastq, options.output )
 
   # perform alignments
     buffsize = 1048576
     try:
         # need to nest try-except in try-finally to handle 2.4
         try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            print "The cmd is %s" % cmd
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp, 'rb' )
+            stderr = ''
             try:
-                tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-                tmp_stderr = open( tmp, 'wb' )
-                print "The cmd is %s" % cmd
-                proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-                returncode = proc.wait()
-                tmp_stderr.close()
-                # get stderr, allowing for case where it's very large
-                tmp_stderr = open( tmp, 'rb' )
-                stderr = ''
-                try:
-                    while True:
-                        stderr += tmp_stderr.read( buffsize )
-                        if not stderr or len( stderr ) % buffsize != 0:
-                            break
-                except OverflowError:
-                    pass
-                tmp_stderr.close()
-                if returncode != 0:
-                    raise Exception, stderr
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if returncode != 0:
+                raise Exception, stderr
+        except Exception, e:
+            raise Exception, 'Error generating alignments. ' + str( e )
+        # remove header if necessary
+        if options.suppressHeader:
+            tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
+            tmp_out_name = tmp_out.name
+            tmp_out.close()
+            try:
+                shutil.move( options.output, tmp_out_name )
             except Exception, e:
-                raise Exception, 'Error generating alignments. ' + str( e )
-            # remove header if necessary
-            if options.suppressHeader == 'true':
-                tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
-                tmp_out_name = tmp_out.name
-                tmp_out.close()
-                try:
-                    shutil.move( options.output, tmp_out_name )
-                except Exception, e:
-                    raise Exception, 'Error moving output file before removing headers. ' + str( e )
-                fout = file( options.output, 'w' )
-                for line in file( tmp_out.name, 'r' ):
-                    if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
-                        fout.write( line )
-                fout.close()
-            # check that there are results in the output file
-            if os.path.getsize( options.output ) > 0:
-                sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
-            else:
-                raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
-        except Exception, e:
-            stop_err( 'The alignment failed.\n' + str( e ) )
+                raise Exception, 'Error moving output file before removing headers. ' + str( e )
+            fout = file( options.output, 'w' )
+            for line in file( tmp_out.name, 'r' ):
+                if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
+                    fout.write( line )
+            fout.close()
+        # check that there are results in the output file
+        if os.path.getsize( options.output ) > 0:
+            sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
+        else:
+            raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
     finally:
         # clean up temp dir
         if os.path.exists( tmp_index_dir ):
diff -r 6820983ba5d5 -r ebb02ba5987c bwa_mem.xml
--- a/bwa_mem.xml	Tue Mar 18 07:49:22 2014 -0400
+++ b/bwa_mem.xml	Fri Mar 21 12:56:15 2014 -0400
@@ -1,26 +1,29 @@
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.7.7">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.8.0">
   <requirements>
     <requirement type="package" version="0.7.7">bwa</requirement>
   </requirements>
   <description></description>
-  <parallelism method="basic"></parallelism>
   <version_command>bwa 2&gt;&amp;1 | grep "Version: " | sed -e 's/Version: //'</version_command>
   <command interpreter="python">
     bwa_mem.py
       --threads="\${GALAXY_SLOTS:-1}"
       --fileSource="${genomeSource.refGenomeSource}"
-      #if $genomeSource.refGenomeSource == "history":
+      #if $genomeSource.refGenomeSource == "history"
         ##build index on the fly
         --ref="${genomeSource.ownFile}"
         --dbkey="${dbkey}"
-      #else:
+      #else
         ##use precomputed indexes
         --ref="${genomeSource.indices.fields.path}"
       #end if
 
       ## input file(s)
       --fastq="${paired.fastq}"
-      #if $paired.sPaired == "paired":
+      #if $paired.sPaired == "single"
+        #if $paired.interPairEnd
+          --interPairEnd
+        #end if
+      #else
         --rfastq="${paired.rfastq}"
       #end if
 
@@ -30,28 +33,60 @@
       ## run parameters
       --genAlignType="${paired.sPaired}"
       --params="${params.source_select}"
-      #if $params.source_select != "pre_set":
-        --minEditDistSeed="${params.minEditDistSeed}"
-        --bandWidth="${params.bandWidth}"
-        --offDiagonal="${params.offDiagonal}"
-        --internalSeeds="${params.internalSeeds}"
-        --seedsOccurrence="${params.seedsOccurrence}"
-        --mateRescue="${params.mateRescue}"
-        --skipPairing="${params.skipPairing}"
-        --seqMatch="${params.seqMatch}"
-        --mismatch="${params.mismatch}"
-        --gapOpen="${params.gapOpen}"
-        --gapExtension="${params.gapExtension}"
-        --clipping="${params.clipping}"
-        --unpairedReadpair="${params.unpairedReadpair}"
-        --interPairEnd="${params.interPairEnd}"
-        --minScore="${params.minScore}"
-        --mark="${params.mark}"
+      #if $params.source_select != "pre_set"
+        #if str($params.minEditDistSeed)
+          --minSeedLength ${params.minEditDistSeed}
+        #end if
+        #if str($params.bandWidth)
+          --bandWidth ${params.bandWidth}
+        #end if
+        #if str($params.offDiagonal)
+          --offDiagonal ${params.offDiagonal}
+        #end if
+        #if str($params.internalSeeds)
+          --internalSeeds ${params.internalSeeds}
+        #end if
+        #if str($params.seedsOccurrence)
+          --seedsOccurrence ${params.seedsOccurrence}
+        #end if
+        #if $params.mateRescue
+          --mateRescue
+        #end if
+        #if $params.skipPairing
+          --skipPairing
+        #end if
+        #if str($params.seqMatch)
+          --seqMatch ${params.seqMatch}
+        #end if
+        #if str($params.mismatch)
+          --mismatch ${params.mismatch}
+        #end if
+        #if str($params.gapOpen)
+          --gapOpen ${params.gapOpen}
+        #end if
+        #if str($params.gapExtension)
+          --gapExtension ${params.gapExtension}
+        #end if
+        #if $params.clipping
+          --clipping "${params.clipping}"
+        #end if
+        #if str($params.unpairedReadpair)
+          --unpairedReadpair ${params.unpairedReadpair}
+        #end if
+        #if str($params.minScore)
+          --minScore ${params.minScore}
+        #end if
+        #if $params.outputAll
+          --outputAll
+        #end if
+        #if $params.mark
+          --mark
+        #end if
 
         #if $params.readGroup.specReadGroup == "yes"
           --rgid="${params.readGroup.rgid}"
           --rgsm="${params.readGroup.rgsm}"
-          --rgpl="${params.readGroup.rgpl}"
+          --rgpl ${params.readGroup.rgpl}
           --rglb="${params.readGroup.rglb}"
           --rgpu="${params.readGroup.rgpu}"
           --rgcn="${params.readGroup.rgcn}"
@@ -65,7 +100,9 @@
       #end if
 
       ## suppress output SAM header
-      --suppressHeader="${suppressHeader}"
+      #if $suppressHeader
+        --suppressHeader
+      #end if
   </command>
 
   <inputs>
@@ -88,11 +125,12 @@
     </conditional>
     <conditional name="paired">
       <param name="sPaired" type="select" label="Is this library mate-paired?">
-        <option value="single">Single-end</option>
+        <option value="single">Single-end or interleaved paired-end</option>
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
         <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
+        <param name="interPairEnd" type="boolean" checked="false" label="FASTQ file consists of interleaved paired-end sequences (-p)" />
       </when>
       <when value="paired">
         <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
@@ -106,43 +144,55 @@
       </param>
       <when value="pre_set" />
       <when value="full">
-        <param name="minEditDistSeed" type="integer" value="19" label="Minimum seed length" />
-        <param name="bandWidth" type="integer" value="100" label="Band width for banded alignment" />
-        <param name="offDiagonal" type="integer" value="100" label="off-diagonal X-dropoff" />
-        <param name="internalSeeds" type="float" value="1.5" label="look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]" />
-        <param name="seedsOccurrence" type="integer" value="10000" label="skip seeds with more than INT occurrences" />
-        <param name="mateRescue" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skip seeds with more than INT occurrences" />
-        <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skpe pairing, mate rescue performed unless -S also in use" />
-        <param name="seqMatch" type="integer" value="1" label="score of a sequence match" />
-        <param name="mismatch" type="integer" value="4" label="penalty for a mismatch" />
-        <param name="gapOpen" type="integer" value="6" label="gap open penalty" />
-        <param name="gapExtension" type="text" value="None" label="gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]" />
-        <param name="clipping" type="integer" value="5" label="penalty for clipping" />
-        <param name="unpairedReadpair" type="integer" value="17" label="penalty for an unpaired read pair" />
-        <param name="interPairEnd" type="boolean" truevalue="True" falsevalue="False" checked="False" label="first query file consists of interleaved paired-end sequences" />
-        <param name="minScore" type="integer" value="30" label="minimum score to output" />
-        <param name="mark" type="boolean" truevalue="True" falsevalue="False" checked="False" label="mark shorter split hits as secondary (for Picard/GATK compatibility)" />
-
+        <param name="minEditDistSeed" type="integer" value="19" optional="true" label="Minimum seed length (-k)" />
+        <param name="bandWidth" type="integer" value="100" optional="true" label="Band width for banded alignment (-w)" />
+        <param name="offDiagonal" type="integer" value="100" optional="true" label="Off-diagonal X-dropoff (-d)" />
+        <param name="internalSeeds" type="float" value="1.5" optional="true" label="Look for internal seeds inside a seed longer than the minimum seed length times this value (-r)" help="This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
+        <param name="seedsOccurrence" type="integer" value="10000" optional="true" label="Skip seeds with more occurrences than this value (-c)" />
+        <param name="mateRescue" type="boolean" checked="false" label="Skip mate rescue (-S)" />
+        <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Skip pairing (-P)" help="In the paired-end mode, perform Smith-Waterman to rescue missing hits only, but do not try to find hits that fit a proper pair" />
+        <param name="seqMatch" type="integer" value="1" optional="true" label="Score for a sequence match (-A)" />
+        <param name="mismatch" type="integer" value="4" optional="true" label="Penalty for a mismatch (-B)" />
+        <param name="gapOpen" type="integer" value="6" optional="true" label="Gap open penalty (-O)" />
+        <param name="gapExtension" type="integer" value="1" optional="true" label="Gap extension penalty (-E)" help="A gap of length k costs {gap open penalty} + k*{this value}" />
+        <param name="clipping" type="text" value="5" optional="true" label="Penalty for clipping (-L)" help="When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced. If two comma-separated numbers are provided, the first is for 5'-end clipping and second for 3'-end clipping">
+          <validator type="regex" message="Invalid clipping, format is INT[,INT]">\d+(,\d+)?$</validator>
+        </param>
+        <param name="unpairedReadpair" type="integer" value="17" optional="true" label="Penalty for an unpaired read pair (-U)" help="" />
+        <param name="minScore" type="integer" value="30" optional="true" label="Minimum score to output (-T)" />
+        <param name="outputAll" type="boolean" checked="false" label="Output all found alignments for single-end or unpaired paired-end reads (-a)" help="These alignments will be flagged as secondary alignments" />
+        <param name="mark" type="boolean" checked="false" label="Mark shorter split hits as secondary (-M)" help="For Picard/GATK compatibility" />
         <conditional name="readGroup">
-          <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
+          <param name="specReadGroup" type="select" label="Specify the read group for this file? (-R)">
             <option value="yes">Yes</option>
             <option value="no" selected="True">No</option>
           </param>
           <when value="yes">
-            <param name="rgid" type="text" size="25" label="[Essential]Read group identifier (ID). 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." help="Required if RG specified. Read group 
-IDs may be modified when merging SAM files in order to handle collisions." />
-            <param name="rgpl" type="text" size="25" label="[Essential]Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, 
-SOLID, HELICOS, IONTORRENT and PACBIO" />
-            <param name="rglb" type="text" size="25" label="[Essential]Library name (LB)" help="Required if RG specified" />
-            <param name="rgsm" type="text" size="25" label="[Essential]Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
+            <param name="rgid" type="text" size="25" label="Read group identifier (ID). 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." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions.">
+              <validator type="empty_field" />
+            </param>
+            <param name="rgpl" type="select" label="Platform/technology used to produce the reads (PL)">
+              <option value="CAPILLARY">CAPILLARY</option>
+              <option value="LS454">LS454</option>
+              <option value="ILLUMINA">ILLUMINA</option>
+              <option value="SOLID">SOLID</option>
+              <option value="HELICOS">HELICOS</option>
+              <option value="IONTORRENT">IONTORRENT</option>
+              <option value="PACBIO">PACBIO</option>
+            </param>
+            <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified">
+              <validator type="empty_field" />
+            </param>
+            <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced">
+              <validator type="empty_field" />
+            </param>
             <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
             <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
             <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
             <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
-            <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each 
-flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by 
-various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
+            <param name="rgfo" type="text" size="25" optional="true" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each flow of each read" help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
+              <validator type="regex">\*|[ACMGRSVTWYHKDBN]+$</validator>
+            </param>
             <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
             <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
             <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
@@ -151,7 +201,7 @@
         </conditional>
       </when>
     </conditional>
-    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
+    <param name="suppressHeader" type="boolean" checked="false" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
   </inputs>
 
   <outputs>
diff -r 6820983ba5d5 -r ebb02ba5987c readme.rst
--- a/readme.rst	Tue Mar 18 07:49:22 2014 -0400
+++ b/readme.rst	Fri Mar 21 12:56:15 2014 -0400
@@ -25,9 +25,10 @@
 Version history
 ---------------
 
-- Release 0: Initial release in the Tool Shed. This is a fork of http://toolshed.g2.bx.psu.edu/view/yufei-luo/bwa_0_7_5 repository with the following changes: Remove .loc file, only .loc.sample should be included. Fix bwa_index.loc.sample file to contain only comments. Add suppressHeader param as in bwa_wrappers. Use $GALAXY_SLOTS environment variable when available. Add <version_command> and <help>. Remove unused import. Fix spacing and typos. Use new recommended citation. Add tool_dependencies.xml . Rename to bwa_mem. Remove definitively colorspace support. Use optparse instead of argparse since Galaxy still supports Python 2.6 .
+- Release 1 (bwa_mem 0.8.0): Rewrite of param handling. interPairEnd param moved to "paired" section. Add param for '-a' option. Remove basic parallelism tag, which does not work with multiple inputs (thanks Björn Grüning for the notice). Simplify Python code.
+- Release 0 (bwa_mem 0.7.7): Initial release in the Tool Shed. This is a fork of http://toolshed.g2.bx.psu.edu/view/yufei-luo/bwa_0_7_5 repository with the following changes: Remove .loc file, only .loc.sample should be included. Fix bwa_index.loc.sample file to contain only comments. Add suppressHeader param as in bwa_wrappers. Use $GALAXY_SLOTS environment variable when available. Add <version_command> and <help>. Remove unused import. Fix spacing and typos. Use new recommended citation. Add tool_dependencies.xml . Rename to bwa_mem. Remove definitively colorspace support. Use optparse instead of argparse since Galaxy still supports Python 2.6 . Add COPYING and readme.rst files.
 
 Development
 -----------
 
-Development is hosted at https://bitbucket.org/nsoranzo/bwa_mem . Contributions and bug reports are very welcome!
+Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!