# HG changeset patch
# User nilshomer
# Date 1307479586 14400
# Node ID de2efe4dda3f6b0a4481d7bd07aa7af460130165

Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

diff -r 000000000000 -r de2efe4dda3f tmap_wrapper_0.0.19/tmap_index.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmap_wrapper_0.0.19/tmap_index.loc.sample	Tue Jun 07 16:46:26 2011 -0400
@@ -0,0 +1,42 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of TMAP indexed sequences data files. You will need
+#to create these data files and then create a tmap_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The tmap_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_path>
+#
+#So, for example, if you had phiX indexed stored in 
+#/depot/data2/galaxy/phiX/base/, 
+#then the tmap_index.loc entry would look like this:
+#
+#phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.fa.* files:
+#
+#-rw-r--r--  1 nilshomer  staff    68B Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.anno
+#-rw-r--r--  1 nilshomer  staff   172M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.bwt
+#-rw-r--r--  1 nilshomer  staff   1.1M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.pac
+#-rw-r--r--  1 nilshomer  staff   172M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rbwt
+#-rw-r--r--  1 nilshomer  staff   1.1M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rpac
+#-rw-r--r--  1 nilshomer  staff   572K Jan 27 15:54 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rsa
+#-rw-r--r--  1 nilshomer  staff   572K Jan 27 15:54 /data/mapping/genomes/DH10B/DH10B.fa.tmap.sa
+#...etc...
+#
+#Your tmap_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files.  For example:
+#
+#phiX174              phiX   phiX174          /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon            hg18   hg18 Canonical   /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full             hg18   hg18 Full        /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa   hg19   hg19             /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r de2efe4dda3f tmap_wrapper_0.0.19/tmap_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmap_wrapper_0.0.19/tmap_wrapper.py	Tue Jun 07 16:46:26 2011 -0400
@@ -0,0 +1,439 @@
+#!/usr/bin/env python
+
+# TODO
+# - map1/map2/map3 specific options
+
+"""
+Runs TMAP on Ion Torrent data.
+Produces a SAM file containing the mappings.
+Works with TMAP version 0.0.19 or higher.
+
+usage: tmap_wrapper.py [options]
+    --threads: The number of threads to use
+    --ref: The reference genome to use or index
+    --fastq: The fastq file to use for the mapping
+    --output: The file to save the output (SAM format)
+    --params: Parameter setting to use (pre_set or full)
+    --fileSource: Whether to use a previously indexed reference sequence or one from history (indexed or history)
+    --matchScore: The match score
+    --mismatchPenalty: The ismatch penalty
+    --gapOpenPenalty: The gap open penalty
+    --gapExtensPenalty: The gap extension penalty
+    --flowPenalty: The flow score penalty
+    --flowOrder: The flow order ([ACGT]{4+} or "sff")
+    --bandWidth: The band width
+    --globalMap: The soft-clipping type (0 - allow on the right and left, 1 - allow on the left, 2 - allow on the right, 3 - do not allow soft-clipping)
+    --duplicateWindow: Remove duplicate alignments from different algorithms within this bp window (-1 to disable)
+    --scoringThreshold: The score threshold divided by the match score 
+    --queueSize: The queue size for the reads
+    --outputFilter: The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)
+    --rgTag: The flag to specify RG tag(s) in the SAM header
+    --rgTagID: The RG ID tag to add to the SAM header
+    --rgTagCN: The RG CN tag to add to the SAM header
+    --rgTagDS: The RG DS tag to add to the SAM header
+    --rgTagDT: The RG DT tag to add to the SAM header
+    --rgTagLB: The RG LB tag to add to the SAM header
+    --rgTagPI: The RG PI tag to add to the SAM header
+    --rgTagPL: The RG PL tag to add to the SAM header
+    --rgTagPU: The RG PU tag to add to the SAM header
+    --rgTagSM: The RG SM tag to add to the SAM header
+    --filterIndependently: Apply the output filter for each algorithm independently
+
+    --map1: Flag to run map1 in the first stage
+    --map1SeedLength: The k-mer length to seed CALs (-1 to disable)
+    --map1SeedMismatches: The maximum number of mismatches in the seed 
+    --map1SecondarySeedLength: The secondary seed length (-1 to disable)
+    --map1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate
+    --map1BaseError: The assumed per-base maximum error rate
+    --map1Mismatches: The maximum number of or (read length) fraction of mismatches 
+    --map1GapOpens: The maximum number of or (read length) fraction of indel starts 
+    --map1GapExtensions: The maximum number of or (read length) fraction of indel extensions 
+    --map1MaxCALsDeletion: The maximum number of CALs to extend a deletion 
+    --map1EndIndels: Indels are not allowed within this number of bps from the end of the read 
+    --map1MaxOptimalCALs: Stop searching when INT optimal CALs have been found 
+    --map1MaxNodes: The maximum number of alignment nodes 
+
+    --map2: Flag to run map2 in the first stage
+    --map2Coefficient: The coefficient of length-threshold adjustment 
+    --map2SeedIntervalSize: The maximum seeding interval size 
+    --map2ZBest: Keep the z-best nodes during prefix trie traversal
+    --map2ReverseTrigger: The # seeds to trigger reverse alignment 
+
+    --map3: Flag to run map3 in the first stage
+    --map3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size) 
+    --map3SeedMaxHits: The maximum number of hits returned by a seed 
+    --map3SeedWindow: The window of bases in which to group seeds 
+    --map3HPEnumeration: The single homopolymer error difference for enumeration 
+    
+    --MAP1: Flag to run MAP1 in the second stage
+    --MAP1SeedLength: The k-mer length to seed CALs (-1 to disable)
+    --MAP1SeedMismatches: The maximum number of mismatches in the seed 
+    --MAP1SecondarySeedLength: The secondary seed length (-1 to disable)
+    --MAP1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate
+    --MAP1BaseError: The assumed per-base maximum error rate
+    --MAP1Mismatches: The maximum number of or (read length) fraction of mismatches 
+    --MAP1GapOpens: The maximum number of or (read length) fraction of indel starts 
+    --MAP1GapExtensions: The maximum number of or (read length) fraction of indel extensions 
+    --MAP1MaxCALsDeletion: The maximum number of CALs to extend a deletion 
+    --MAP1EndIndels: Indels are not allowed within this number of bps from the end of the read 
+    --MAP1MaxOptimalCALs: Stop searching when INT optimal CALs have been found 
+    --MAP1MaxNodes: The maximum number of alignment nodes 
+
+    --MAP2: Flag to run MAP2 in the second stage
+    --MAP2Coefficient: The coefficient of length-threshold adjustment 
+    --MAP2SeedIntervalSize: The maximum seeding interval size 
+    --MAP2ZBest: Keep the z-best nodes during prefix trie traversal
+    --MAP2ReverseTrigger: The # seeds to trigger reverse alignment 
+
+    --MAP3: Flag to run MAP3 in the second stage
+    --MAP3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size) 
+    --MAP3SeedMaxHits: The maximum number of hits returned by a seed 
+    --MAP3SeedWindow: The window of bases in which to group seeds 
+    --MAP3HPEnumeration: The single homopolymer error difference for enumeration 
+
+    --suppressHeader: Suppress header
+    --dbkey: Dbkey for reference genome
+    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
+"""
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def map1_parse( map1SeedLength, map1SeedMismatches, \
+        map1SecondarySeedLength, map1NumEdits, \
+        map1BaseError, map1Mismatches, \
+        map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
+        map1EndIndels, map1MaxOptimalCALs, map1MaxNodes ):
+    return '-l %s -s %s -L %s -p %s -P %s -m %s -o %s -e %s -d %s -i %s -b %s -Q %s' % \
+            (map1SeedLength, map1SeedMismatches, \
+            map1SecondarySeedLength, map1NumEdits, \
+            map1BaseError, map1Mismatches, \
+            map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
+            map1EndIndels, map1MaxOptimalCALs, map1MaxNodes )
+
+def map2_parse( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger ):
+    return '-c %s -S %s -b %s -N %s' % ( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger )
+
+def map3_parse( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration ):
+    return '-l %s -S %s -b %s -H %s' % ( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration )
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    # Global options
+    parser.add_option( '--threads', dest='threads', help='The number of threads to use' )
+    parser.add_option( '--ref', dest='ref', help='The reference genome to use or index' )
+    parser.add_option( '--fastq', dest='fastq', help='The fastq file to use for the mapping' )
+    parser.add_option( '--output', dest='output', help='The file to save the output (SAM format)' )
+    parser.add_option( '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
+    parser.add_option( '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
+    parser.add_option( '--mapall', dest='mapall', help='Flag indicating if mapall options are present')
+    parser.add_option( '--matchScore', dest='matchScore', help='The match score' )
+    parser.add_option( '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
+    parser.add_option( '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
+    parser.add_option( '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
+    parser.add_option( '--flowPenalty', dest='flowPenalty', help='Flow score penalty' )
+    parser.add_option( '--flowOrder', dest='flowOrder', help='Flow order' )
+    parser.add_option( '--bandWidth', dest='bandWidth', help='The band width' )
+    parser.add_option( '--globalMap', dest='globalMap', help='Map the full read (no soft-clipping)' )
+    parser.add_option( '--duplicateWindow', dest='duplicateWindow', help='Remove duplicate alignments from different algorithms within this bp window (-1 to disable)' )
+    parser.add_option( '--scoringThreshold', dest='scoringThreshold', help='The score threshold divided by the match score ' )
+    parser.add_option( '--queueSize', dest='queueSize', help='The queue size for the reads' )
+    parser.add_option( '--outputFilter', dest='outputFilter', help='The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)' )
+    parser.add_option( '--rgTag', dest='rgTag', help='The flag to specify RG tag(s) in the SAM header' )
+    parser.add_option( '--rgTagID', dest='rgTagID', default='', help='The RG ID to add to the SAM header' )
+    parser.add_option( '--rgTagCN', dest='rgTagCN', default='', help='The RG CN to add to the SAM header' )
+    parser.add_option( '--rgTagDS', dest='rgTagDS', default='', help='The RG DS to add to the SAM header' )
+    parser.add_option( '--rgTagDT', dest='rgTagDT', default='', help='The RG DT to add to the SAM header' )
+    parser.add_option( '--rgTagLB', dest='rgTagLB', default='', help='The RG LB to add to the SAM header' )
+    parser.add_option( '--rgTagPI', dest='rgTagPI', default='', help='The RG PI to add to the SAM header' )
+    parser.add_option( '--rgTagPL', dest='rgTagPL', default='', help='The RG PL to add to the SAM header' )
+    parser.add_option( '--rgTagPU', dest='rgTagPU', default='', help='The RG PU to add to the SAM header' )
+    parser.add_option( '--rgTagSM', dest='rgTagSM', default='', help='The RG SM to add to the SAM header' )
+    parser.add_option( '--filterIndependently', dest='filterIndependently', help='Apply the output filter for each algorithm independently' )
+    parser.add_option( '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    parser.add_option( '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
+    parser.add_option( '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
+    # map 1 - stage 1
+    parser.add_option( '--map1', dest='map1', help='True if map1 should be run in the first stage' )
+    parser.add_option( '--map1SeedLength', dest='map1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
+    parser.add_option( '--map1SeedMismatches', dest='map1SeedMismatches', help='The maximum number of mismatches in the seed ' )
+    parser.add_option( '--map1SecondarySeedLength', dest='map1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )
+    parser.add_option( '--map1NumEdits', dest='map1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )
+    parser.add_option( '--map1BaseError', dest='map1BaseError', help='The assumed per-base maximum error rate' )
+    parser.add_option( '--map1Mismatches', dest='map1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
+    parser.add_option( '--map1GapOpens', dest='map1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
+    parser.add_option( '--map1GapExtensions', dest='map1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
+    parser.add_option( '--map1MaxCALsDeletion', dest='map1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
+    parser.add_option( '--map1EndIndels', dest='map1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
+    parser.add_option( '--map1MaxOptimalCALs', dest='map1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
+    parser.add_option( '--map1MaxNodes', dest='map1MaxNodes', help='The maximum number of alignment nodes ' )
+    # map 2 - stage 1
+    parser.add_option( '--map2', dest='map2', help='True if map2 should be run in the first stage' )
+    parser.add_option( '--map2Coefficient', dest='map2Coefficient', help='The coefficient of length-threshold adjustment ' )
+    parser.add_option( '--map2SeedIntervalSize', dest='map2SeedIntervalSize', help='The maximum seeding interval size ' )
+    parser.add_option( '--map2ZBest', dest='map2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
+    parser.add_option( '--map2ReverseTrigger', dest='map2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
+    # map 3 - stage 1
+    parser.add_option( '--map3', dest='map3', help='True if map3 should be run in the first stage' )
+    parser.add_option( '--map3SeedLength', dest='map3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
+    parser.add_option( '--map3SeedMaxHits', dest='map3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
+    parser.add_option( '--map3SeedWindow', dest='map3SeedWindow', help='The window of bases in which to group seeds ' )
+    parser.add_option( '--map3HPEnumeration', dest='map3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
+    # map 1 - stage 2
+    parser.add_option( '--MAP1', dest='MAP1', help='True if map1 should be run in the second stage' )
+    parser.add_option( '--MAP1SeedLength', dest='MAP1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
+    parser.add_option( '--MAP1SeedMismatches', dest='MAP1SeedMismatches', help='The maximum number of mismatches in the seed ' )
+    parser.add_option( '--MAP1SecondarySeedLength', dest='MAP1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )
+    parser.add_option( '--MAP1NumEdits', dest='MAP1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )
+    parser.add_option( '--MAP1BaseError', dest='MAP1BaseError', help='The assumed per-base maximum error rate' )
+    parser.add_option( '--MAP1Mismatches', dest='MAP1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
+    parser.add_option( '--MAP1GapOpens', dest='MAP1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
+    parser.add_option( '--MAP1GapExtensions', dest='MAP1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
+    parser.add_option( '--MAP1MaxCALsDeletion', dest='MAP1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
+    parser.add_option( '--MAP1EndIndels', dest='MAP1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
+    parser.add_option( '--MAP1MaxOptimalCALs', dest='MAP1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
+    parser.add_option( '--MAP1MaxNodes', dest='MAP1MaxNodes', help='The maximum number of alignment nodes ' )
+    # map 2 - stage 2
+    parser.add_option( '--MAP2', dest='MAP2', help='True if map2 should be run in the second stage' )
+    parser.add_option( '--MAP2Coefficient', dest='MAP2Coefficient', help='The coefficient of length-threshold adjustment ' )
+    parser.add_option( '--MAP2SeedIntervalSize', dest='MAP2SeedIntervalSize', help='The maximum seeding interval size ' )
+    parser.add_option( '--MAP2ZBest', dest='MAP2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
+    parser.add_option( '--MAP2ReverseTrigger', dest='MAP2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
+    # map 3 - stage 2
+    parser.add_option( '--MAP3', dest='MAP3', help='True if map3 should be run in the second stage' )
+    parser.add_option( '--MAP3SeedLength', dest='MAP3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
+    parser.add_option( '--MAP3SeedMaxHits', dest='MAP3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
+    parser.add_option( '--MAP3SeedWindow', dest='MAP3SeedWindow', help='The window of bases in which to group seeds ' )
+    parser.add_option( '--MAP3HPEnumeration', dest='MAP3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
+    # parse the options
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='tmap --version 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'TMAP %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine TMAP version\n' )
+
+    fastq = options.fastq
+
+    # make temp directory for placement of indices
+    tmp_index_dir = tempfile.mkdtemp()
+    tmp_dir = tempfile.mkdtemp()
+
+    # index if necessary
+    if options.fileSource == 'history' and not options.do_not_build_index:
+        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+        ref_file_name = ref_file.name
+        ref_file.close()
+        os.symlink( options.ref, ref_file_name )
+        cmd1 = 'tmap index -f %s -v ' % ( ref_file_name )
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_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 = ''
+            buffsize = 1048576
+            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
+        except Exception, e:
+            # clean up temp dirs
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            if os.path.exists( tmp_dir ):
+                shutil.rmtree( tmp_dir )
+            stop_err( 'Error indexing reference sequence. ' + str( e ) )
+    else:
+        ref_file_name = options.ref
+
+    # set up mapping and generate mapping command options
+    if options.params == 'pre_set':
+        mapall_options = '-n %s' % ( options.threads )
+        map1_options = 'map1'
+        map2_options = 'map2'
+        map3_options = 'map3'
+        MAP1_options = ''
+        MAP2_options = ''
+        MAP3_options = ''
+    else:
+        # mapall options
+        if options.rgTag == 'true':
+            rgTag = ''
+            if options.rgTagID != '':
+                rgTag += '-R "ID:' + options.rgTagID + '" '
+            if options.rgTagCN != '':
+                rgTag += '-R "CN:' + options.rgTagCN + '" '
+            if options.rgTagDS != '':
+                rgTag += '-R "DS:' + options.rgTagDS + '" '
+            if options.rgTagDT != '':
+                rgTag += '-R "DT:' + options.rgTagDT + '" '
+            if options.rgTagLB != '':
+                rgTag += '-R "LB:' + options.rgTagLB + '" '
+            if options.rgTagPI != '':
+                rgTag += '-R "PI:' + options.rgTagPI + '" '
+            if options.rgTagPL != '':
+                rgTag += '-R "PL:' + options.rgTagPL + '" '
+            if options.rgTagPU != '':
+                rgTag += '-R "PU:' + options.rgTagPU + '" '
+            if options.rgTagSM != '':
+                rgTag += '-R "SM:' + options.rgTagSM + '" '
+            rgTag.rstrip(' ')
+        else:
+            rgTag = ''
+        if None != options.flowOrder and '' != options.flowOrder:
+            flowOrder = '-x ' + options.flowOrder
+        else:
+            flowOrder = ''
+        if options.filterIndependently == 'true':
+            filterIndependently = '-I'
+        else:
+            filterIndependently = ''
+        if options.mapall == 'true':
+            mapall_options = '-A %s -M %s -O %s -E %s -X %s %s %s -W %s -T %s -q %s -n %s -a %s %s %s' % \
+                    ( options.matchScore, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
+                            options.flowPenalty, flowOrder,
+                            options.globalMap, options.duplicateWindow, options.scoringThreshold, options.queueSize,
+                            options.threads, options.outputFilter, rgTag, filterIndependently )
+        else:
+            mapall_options = ''
+
+        # map1 - stage one
+        if options.map1 == 'true':
+            map1_options = 'map1 %s' % \
+                    map1_parse( options.map1SeedLength, options.map1SeedMismatches, \
+                    options.map1SecondarySeedLength, options.map1NumEdits, \
+                    options.map1BaseError, options.map1Mismatches, \
+                    options.map1GapOpens, options.map1GapExtensions, options.map1MaxCALsDeletion, \
+                    options.map1EndIndels, options.map1MaxOptimalCALs, options.map1MaxNodes )
+        else:
+            map1_options = ''
+        # map2 - stage one
+        if options.map2 == 'true':
+            map2_options = 'map2 %s' % \
+                    map2_parse( options.map2Coefficient, options.map2SeedIntervalSize, \
+                    options.map2ZBest, options.map2ReverseTrigger )
+        else:
+            map2_options = ''
+        # map3 - stage one
+        if options.map3 == 'true':
+            map3_options = 'map3 %s' % \
+                    map3_parse( options.map3SeedLength, options.map3SeedMaxHits, \
+                    options.map3SeedWindow, options.map3HPEnumeration )
+        else:
+            map3_options = ''
+        # map1 - stage two
+        if options.MAP1== 'true':
+            MAP1_options = 'MAP1 %s' % \
+                    map1_parse( options.MAP1SeedLength, options.MAP1SeedMismatches, \
+                    options.MAP1SecondarySeedLength, options.MAP1NumEdits, \
+                    options.MAP1BaseError, options.MAP1Mismatches, \
+                    options.MAP1GapOpens, options.MAP1GapExtensions, options.MAP1MaxCALsDeletion, \
+                    options.MAP1EndIndels, options.MAP1MaxOptimalCALs, options.MAP1MaxNodes )
+        else:
+            MAP1_options = ''
+        # map2 - stage two
+        if options.MAP2 == 'true':
+            MAP2_options = 'MAP2 %s' % \
+                    map2_parse( options.MAP2Coefficient, options.MAP2SeedIntervalSize, \
+                    options.MAP2ZBest, options.MAP2ReverseTrigger )
+        else:
+            MAP2_options = ''
+        # map3 - stage two
+        if options.MAP3 == 'true':
+            MAP3_options = 'MAP3 %s' % \
+                    MAP3_parse( options.MAP3SeedLength, options.MAP3SeedMaxHits, \
+                    options.MAP3SeedWindow, options.MAP3HPEnumeration )
+        else:
+            MAP3_options = ''
+
+    #mapping_cmds 
+    # prepare actual mapping and generate mapping commands
+    cmd2 = 'tmap mapall -f %s -r %s -F fastq %s -v %s %s %s %s %s %s > %s' % \
+            ( ref_file_name, fastq, mapall_options, 
+                    map1_options, map2_options, map3_options,
+                    MAP1_options, MAP2_options, MAP3_options,
+                    options.output )
+    # perform alignments
+    buffsize = 1048576
+    try:
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            # align
+            try:
+                tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+                tmp_stderr = open( tmp, 'wb' )
+                proc = subprocess.Popen( args=cmd2, 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
+            except Exception, e:
+                raise Exception, 'Error mapping sequence. ' + 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( 'TMAP completed' )
+            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 ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_index_dir ):
+            shutil.rmtree( tmp_index_dir )
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()
diff -r 000000000000 -r de2efe4dda3f tmap_wrapper_0.0.19/tmap_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmap_wrapper_0.0.19/tmap_wrapper.xml	Tue Jun 07 16:46:26 2011 -0400
@@ -0,0 +1,450 @@
+<tool id="tmap_wrapper" name="Map with TMAP" version="0.0.19">
+	<description>for Ion Torrent</description>
+	<parallelism method="basic"></parallelism>
+	<command interpreter="python">
+		tmap_wrapper.py 
+
+		## reference source
+		--fileSource=$genomeSource.refGenomeSource
+		#if $genomeSource.refGenomeSource == "history":
+			##build index on the fly
+			--ref="${genomeSource.ownFile}"
+			--dbkey=$dbkey
+		#else:
+			##use precomputed indexes
+			--ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'tmap_indexes' ].get_fields() )[0][-1] }"
+			--do_not_build_index
+		#end if
+
+		## input fastq
+		--fastq=$input
+
+		## output file
+		--output=$output
+
+		## run parameters
+		--params=$params.source_select
+		#if $params.source_select != "pre_set":
+			--mapall=$params.mapall.source_select
+			#if $params.mapall.source_select == "true":
+				--threads=$params.mapall.threads
+				--matchScore=$params.mapall.matchScore
+				--mismatchPenalty=$params.mapall.mismatchPenalty
+				--gapOpenPenalty=$params.mapall.gapOpenPenalty
+				--gapExtensPenalty=$params.mapall.gapExtensPenalty
+				--flowPenalty=$params.mapall.flowPenalty
+				--flowOrder=$params.mappll.flowOrder
+				--bandWidth=$params.mapall.bandWidth
+				--globalMap=$params.mapall.globalMap
+				--duplicateWindow=$params.mapall.duplicateWindow
+				--scoringThreshold=$params.mapall.scoringThreshold
+				--queueSize=$params.mapall.queueSize
+				--outputFilter=$params.mapall.outputFilter
+				--rgTag=$params.mapall.rgTag.source_select
+				#if $params.mapall.rgTag.source_select == "true":
+					--rgTagID=$params.mapall.rgTag.rgTagID
+					--rgTagCN=$params.mapall.rgTag.rgTagCN
+					--rgTagDS=$params.mapall.rgTag.rgTagDS
+					--rgTagDT=$params.mapall.rgTag.rgTagDT
+					--rgTagLB=$params.mapall.rgTag.rgTagLB
+					--rgTagPI=$params.mapall.rgTag.rgTagPI
+					--rgTagPL=$params.mapall.rgTag.rgTagPL
+					--rgTagPU=$params.mapall.rgTag.rgTagPU
+					--rgTagSM=$params.mapall.rgTag.rgTagSM
+				#end if
+				--filterIndependently=$params.mapall.filterIndependently 
+			#end if
+			--map1=$params.map1.source_select
+			#if $params.map1.source_select == "true":
+				--map1SeedLength=$params.map1.map1SeedLength
+				--map1SeedMismatches=$params.map1.map1SeedMismatches
+				--map1SecondarySeedLength=$params.map1.map1SecondarySeedLength
+				--map1NumEdits=$params.map1.map1NumEdits
+				--map1BaseError=$params.map1.map1BaseError
+				--map1Mismatches=$params.map1.map1Mismatches
+				--map1GapOpens=$params.map1.map1GapOpens
+				--map1GapExtensions=$params.map1.map1GapExtensions
+				--map1MaxCALsDeletion=$params.map1.map1MaxCALsDeletion
+				--map1EndIndels=$params.map1.map1EndIndels
+				--map1MaxOptimalCALs=$params.map1.map1MaxOptimalCALs
+				--map1MaxNodes=$params.map1.map1MaxNodes
+			#end if
+			--map2=$params.map2.source_select
+			#if $params.map2.source_select == "true":
+				--map2Coefficient=$params.map2.map2Coefficient
+				--map2SeedIntervalSize=$params.map2.map2SeedIntervalSize
+				--map2ZBest=$params.map2.map2ZBest
+				--map2ReverseTrigger=$params.map2.map2ReverseTrigger
+			#end if
+			--map3=$params.map3.source_select
+			#if $params.map3.source_select == "true":
+				--map3SeedLength=$params.map3.map3SeedLength
+				--map3SeedMaxHits=$params.map3.map3SeedMaxHits
+				--map3SeedWindow=$params.map3.map3SeedWindow
+				--map3HPEnumeration=$params.map3.map3HPEnumeration
+			#end if
+			--MAP1=$params.MAP1.source_select
+			#if $params.MAP1.source_select == "true":
+				--MAP1SeedLength=$params.MAP1.MAP1SeedLength
+				--MAP1SeedMismatches=$params.MAP1.MAP1SeedMismatches
+				--MAP1SecondarySeedLength=$params.MAP1.MAP1SecondarySeedLength
+				--MAP1NumEdits=$params.MAP1.MAP1NumEdits
+				--MAP1BaseError=$params.MAP1.MAP1BaseError
+				--MAP1Mismatches=$params.MAP1.MAP1Mismatches
+				--MAP1GapOpens=$params.MAP1.MAP1GapOpens
+				--MAP1GapExtensions=$params.MAP1.MAP1GapExtensions
+				--MAP1MaxCALsDeletion=$params.MAP1.MAP1MaxCALsDeletion
+				--MAP1EndIndels=$params.MAP1.MAP1EndIndels
+				--MAP1MaxOptimalCALs=$params.MAP1.MAP1MaxOptimalCALs
+				--MAP1MaxNodes=$params.MAP1.MAP1MaxNodes
+			#end if
+			--MAP2=$params.MAP2.source_select
+			#if $params.MAP2.source_select == "true":
+				--MAP2Coefficient=$params.MAP2.MAP2Coefficient
+				--MAP2SeedIntervalSize=$params.MAP2.MAP2SeedIntervalSize
+				--MAP2ZBest=$params.MAP2.MAP2ZBest
+				--MAP2ReverseTrigger=$params.MAP2.MAP2ReverseTrigger
+			#end if
+			--MAP3=$params.MAP3.source_select
+			#if $params.MAP3.source_select == "true":
+				--MAP3SeedLength=$params.MAP3.MAP3SeedLength
+				--MAP3SeedMaxHits=$params.MAP3.MAP3SeedMaxHits
+				--MAP3SeedWindow=$params.MAP3.MAP3SeedWindow
+				--MAP3HPEnumeration=$params.MAP3.MAP3HPEnumeration
+			#end if
+		#else:
+			--threads="4"
+			--map1="false"
+			--map2="false"
+			--map3="false"
+			--MAP1="false"
+			--MAP2="false"
+			--MAP3="false"
+		#end if
+
+		## suppress output SAM header
+		--suppressHeader=$suppressHeader
+  </command>
+  <requirements>
+	  <requirement type='package'>tmap</requirement>
+  </requirements>
+  <inputs>
+	  <conditional name="genomeSource">
+		  <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+			  <option value="indexed">Use a built-in index</option>
+			  <option value="history">Use one from the history</option>
+		  </param>
+		  <when value="indexed">
+			  <param name="indices" type="select" label="Select a reference genome">
+				  <options from_data_table="tmap_indexes">
+					  <filter type="sort_by" column="3" />
+					  <validator type="no_options" message="No indexes are available for the selected input dataset" />
+				  </options>
+			  </param>
+		  </when>
+		  <when value="history">
+			  <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+		  </when>
+	  </conditional>
+	  <param name="input" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
+	  <conditional name="params">
+		  <param name="source_select" type="select" label="TMAP settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List">
+			  <option value="pre_set">Commonly Used</option>
+			  <option value="full">Full Parameter List</option>
+		  </param>
+		  <when value="pre_set" />
+		  <when value="full">
+			  <conditional name="mapall">
+				  <param name="source_select" type="select" label="Global options to use">
+					  <option value="false" selected="true">Commonly Used</option>
+					  <option value="true">Full Parameter List</option>
+				  </param>
+				  <when value="false" />
+				  <when value="true">
+					  <param name="threads" type="integer" value="4" label="The number of threads (-n)" />
+					  <param name="matchScore" type="integer" value="3" label="Match score (-A)" />
+					  <param name="mismatchPenalty" type="integer" value="5" label="Mismatch penalty (-M)" />
+					  <param name="gapOpenPenalty" type="integer" value="2" label="Gap open penalty (-O)" />
+					  <param name="gapExtensPenalty" type="integer" value="2" label="Gap extension penalty (-E)" />
+					  <param name="flowPenalty" type="integer" value="2" label="The score penalty (-X)" />
+					  <param name="flowOrder" type="text" value="" label="The flow order ([ACGT]{4+} or sff" />
+					  <param name="bandWidth" type="integer" value="50" label="The band width (-w)" />
+					  <param name="globalMap" type="integer" value="2" label="The soft clipping type (-g)" help="The soft-clipping type (0 - allow on the right and left, 1 - allow on the left, 2 - allow on the right, 3 - do not allow soft-clipping)" />
+					  <param name="duplicateWindow" type="integer" value="128" label="The duplicate window (-W)" help="Remove duplicate alignments from different algorithms within this bp window (-1 to disable)"/>
+					  <param name="scoringThreshold" type="integer" value="1" label="The scoring threshold (-T)" help="The score threshold divided by the match score" />
+					  <param name="queueSize" type="integer" value="262144" label="The queue size (-q)" help="The queue size for the reads" />
+					  <param name="outputFilter" type="integer" value="1" label="The output filter (-a)" help="The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)" />
+					  <conditional name="rgTag">
+						  <param name="source_select" type="select" label="Include Custom Read Group Tags">
+							  <option value="false" selected="true">Default</option>
+							  <option value="true">Custom</option>
+						  </param>
+						  <when value="false" />
+						  <when value="true">
+							  <param name="rgTagID" type="text" value="" label="The Read Group ID (-R)" help="The RG ID used in the RG record in the SAM header" />
+							  <param name="rgTagCN" type="text" value="" label="The Read Group CN (-R)" help="The RG CN used in the RG record in the SAM header" />
+							  <param name="rgTagDS" type="text" value="" label="The Read Group DS (-R)" help="The RG DS used in the RG record in the SAM header" />
+							  <param name="rgTagDT" type="text" value="" label="The Read Group DT (-R)" help="The RG DT used in the RG record in the SAM header" />
+							  <param name="rgTagLB" type="text" value="" label="The Read Group LB (-R)" help="The RG LB used in the RG record in the SAM header" />
+							  <param name="rgTagPI" type="text" value="" label="The Read Group PI (-R)" help="The RG PI used in the RG record in the SAM header" />
+							  <param name="rgTagPL" type="text" value="" label="The Read Group PL (-R)" help="The RG PL used in the RG record in the SAM header" />
+							  <param name="rgTagPU" type="text" value="" label="The Read Group PU (-R)" help="The RG PU used in the RG record in the SAM header" />
+							  <param name="rgTagSM" type="text" value="" label="The Read Group SM (-R)" help="The RG SM used in the RG record in the SAM header" />
+						  </when>
+					  </conditional>
+					  <param name="filterIndependently" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Filter algorithm independently (-I)" help="apply the output filter for each algorithm separately" />
+				  </when>
+			  </conditional>
+			  <conditional name="map1">
+				  <param name="source_select" type="select" label="Map1 Stage One" help="Turn on mapping algorithm #1 in the first stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="map1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
+					  <param name="map1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
+					  <param name="map1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
+					  <param name="map1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
+					  <param name="map1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
+					  <param name="map1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
+					  <param name="map1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
+					  <param name="map1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
+					  <param name="map1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
+					  <param name="map1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
+					  <param name="map1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
+					  <param name="map1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+			  <conditional name="map2">
+				  <param name="source_select" type="select" label="Map2 Stage One" help="Turn on mapping algorithm #2 in the first stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="map2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
+					  <param name="map2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
+					  <param name="map2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
+					  <param name="map2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+			  <conditional name="map3">
+				  <param name="source_select" type="select" label="Map3 Stage One" help="Turn on mapping algorithm #3 in the first stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="map3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
+					  <param name="map3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
+					  <param name="map3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
+					  <param name="map3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+			  <conditional name="MAP1">
+				  <param name="source_select" type="select" label="Map1 Stage Two" help="Turn on mapping algorithm #1 in the second stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="MAP1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
+					  <param name="MAP1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
+					  <param name="MAP1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
+					  <param name="MAP1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
+					  <param name="MAP1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
+					  <param name="MAP1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
+					  <param name="MAP1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
+					  <param name="MAP1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
+					  <param name="MAP1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
+					  <param name="MAP1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
+					  <param name="MAP1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
+					  <param name="MAP1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+			  <conditional name="MAP2">
+				  <param name="source_select" type="select" label="Map2 Stage Two" help="Turn on mapping algorithm #2 in the second stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="MAP2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
+					  <param name="MAP2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
+					  <param name="MAP2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
+					  <param name="MAP2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+			  <conditional name="MAP3">
+				  <param name="source_select" type="select" label="Map3 Stage Two" help="Turn on mapping algorithm #3 in the second stage">
+					  <option value="true">Turn On</option>
+					  <option value="false" selected="true">Turn Off</option>
+				  </param>
+				  <when value="true">
+					  <param name="MAP3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
+					  <param name="MAP3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
+					  <param name="MAP3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
+					  <param name="MAP3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
+				  </when>
+				  <when value="false" />
+			  </conditional>
+		  </when>
+	  </conditional>
+	  <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="TMAP produces SAM with several lines of header information" />
+  </inputs>
+  <outputs>
+	  <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+		  <actions>
+			  <conditional name="genomeSource.refGenomeSource">
+				  <when value="indexed">
+					  <action type="metadata" name="dbkey">
+						  <option type="from_data_table" name="tmap_indexes" column="0">
+							  <filter type="param_value" ref="genomeSource.indices" column="1"/>
+						  </option>
+					  </action>
+				  </when>
+			  </conditional>
+		  </actions>
+	  </data>
+  </outputs>
+  <help>
+
+**What it does**
+
+TMAP is a fast light-weight tool that aligns DNA sequences (small queries) to a sequence database (large sequences), such as the human reference genome. TMAP follows a two-stage approach, with a set of algorithms and associated settings for each stage. If there are no mappings for a read by applying the algorithms in the first stage, then the algorithms in the second stage are applied. For example, a set of algorithms to quickly align near-perfect reads may be used in the first stage, while a set of sensitive algorithms may be used to map difficult reads in the second stage.
+ 
+It combines multiple mapping algorithms to give sensitive and accurate alignments quickly.  It uses three core algorithms, BWA-short, BWA-long, and a variant of the SSAHA algorithm. These algorithms are described in the following publications:
+ - Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
+ - Li, H. and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler
+ - Ning, Z., Cox, A., and Mullikin, J. (2001). SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725–1729.
+
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
+
+ .. __: http://www.iontorrent.com/
+
+------
+
+**Input formats**
+
+TMAP accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
+
+------
+
+**A Note on Built-in Reference Genomes**
+
+Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+
+------
+
+**Outputs**
+
+The output is in SAM format, and has the following columns::
+
+    Column  Description
+  --------  --------------------------------------------------------
+  1  QNAME  Query (pair) NAME
+  2  FLAG   bitwise FLAG
+  3  RNAME  Reference sequence NAME
+  4  POS    1-based leftmost POSition/coordinate of clipped sequence
+  5  MAPQ   MAPping Quality (Phred-scaled)
+  6  CIGAR  extended CIGAR string
+  7  MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
+  8  MPOS   1-based Mate POSition
+  9  ISIZE  Inferred insert SIZE
+  10 SEQ    query SEQuence on the same strand as the reference
+  11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
+  12 OPT    variable OPTional fields in the format TAG:VTYPE:VALU
+  
+The flags are as follows::
+
+    Flag  Description
+  ------  -------------------------------------
+  0x0001  the read is paired in sequencing
+  0x0002  the read is mapped in a proper pair
+  0x0004  the query sequence itself is unmapped
+  0x0008  the mate is unmapped
+  0x0010  strand of the query (1 for reverse)
+  0x0020  strand of the mate
+  0x0040  the read is the first read in a pair
+  0x0080  the read is the second read in a pair
+  0x0100  the alignment is not primary
+
+It looks like this (scroll sideways to see the entire example)::
+
+  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
+  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
+  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
+
+-------
+
+**TMAP settings**
+
+All of the options have a default value. You can change most of them. Most of the options in TMAP have been implemented here.
+
+------
+
+**TMAP parameter list**
+
+This is an exhaustive list of TMAP options implemented here:
+
+For the **global** options::
+
+  -A INT      score for a match [5]
+  -M INT      the mismatch penalty [3]
+  -O INT      the indel start penalty [3]
+  -E INT      the indel extend penalty [1]
+  -X INT      the flow score penalty [7]
+  -w INT      the band width [50]
+  -g          map the full read [false]
+  -W INT      remove duplicate alignments from different algorithms within this bp window (-1 to disable) [128]
+  -T INT      score threshold divided by the match score [30]
+  -q INT      the queue size for the reads (-1 disables) [65536]
+  -n INT      the number of threads [1]
+  -a INT      output filter [1]
+		  0 - unique best hits
+ 		  1 - random best hit
+ 		  2 - all best hits
+ 		  3 - all alignments
+  -R STRING   the RG tags to add to the SAM header [(null)]
+
+For **mapall** options::
+
+  -I          apply the output filter for each algorithm separately [false]
+ 
+For **map1** options::
+
+  -l INT      the k-mer length to seed CALs (-1 to disable) [32]
+  -s INT      maximum number of mismatches in the seed [3]
+  -m NUM      maximum number of or (read length) fraction of mismatches [number: 2]
+  -o NUM      maximum number of or (read length) fraction of indel starts [number: 1]
+  -e NUM      maximum number of or (read length) fraction of indel extensions [number: 6]
+  -d INT      the maximum number of CALs to extend a deletion [10]
+  -i INT      indels are not allowed within INT number of bps from the end of the read [5]
+  -b INT      stop searching when INT optimal CALs have been found [32]
+  -Q INT      maximum number of alignment nodes [2000000]
+ 
+For **map2** options::
+
+  -c FLOAT    coefficient of length-threshold adjustment [5.5]
+  -S INT      maximum seeding interval size [3]
+  -b INT      Z-best [1]
+  -N INT      # seeds to trigger reverse alignment [5]
+ 
+For **map3** options::
+
+  -l INT      the k-mer length to seed CALs (-1 tunes to the genome size) [-1]
+  -S INT      the maximum number of hits returned by a seed [8]
+  -b INT      the window of bases in which to group seeds [50]
+  -H INT      single homopolymer error difference for enumeration [0]
+
+  </help>
+</tool>
+
+