3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f31e7076b885/ changeset: f31e7076b885 branch: updates-for-tophat-1.3.1+ user: jjohnson date: 2011-11-03 16:30:36 summary: Tophat - update tool wrappers for Tophat version 1.3.1+ affected #: 3 files diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -40,15 +40,18 @@ -g $singlePaired.sParams.max_multihits --min-segment-intron $singlePaired.sParams.min_segment_intron --max-segment-intron $singlePaired.sParams.max_segment_intron + --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches --seg-mismatches=$singlePaired.sParams.seg_mismatches --seg-length=$singlePaired.sParams.seg_length --library-type=$singlePaired.sParams.library_type ## Indel search. #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes": - --allow-indels + ## --allow-indels --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length + #else: + --no-novel-indels #end if ## Supplying junctions parameters. @@ -99,15 +102,18 @@ -g $singlePaired.pParams.max_multihits --min-segment-intron $singlePaired.pParams.min_segment_intron --max-segment-intron $singlePaired.pParams.max_segment_intron + --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches --seg-mismatches=$singlePaired.pParams.seg_mismatches --seg-length=$singlePaired.pParams.seg_length --library-type=$singlePaired.pParams.library_type ## Indel search. #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes": - --allow-indels + ## --allow-indels --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length + #else: + --no-novel-indels #end if ## Supplying junctions parameters. @@ -203,6 +209,7 @@ <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> @@ -309,6 +316,7 @@ <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /><!-- Options for supplying own junctions. --> diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -29,10 +29,11 @@ help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' ) parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' ) parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) + parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' ) parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' ) - parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.' ) + parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)' ) parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' ) parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' ) @@ -50,6 +51,7 @@ sequence, inclusive.') parser.add_option( '', '--no-novel-juncs', action="store_true", dest='no_novel_juncs', help="Only look for junctions indicated in the \ supplied GFF file. (ignored without -G)") + parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.") # Types of search. parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.') parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)') @@ -160,12 +162,16 @@ opts += ' --no-novel-juncs' if options.library_type: opts += ' --library-type %s' % options.library_type - if options.allow_indels: - # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. - opts += ' --allow-indels' - #opts += ' --max-insertion-length %i --max-deletion-length %i' % ( int( options.max_insertion_length ), int( options.max_deletion_length ) ) + if options.no_novel_indels: + opts += ' --no-novel-indels' + else: + if options.max_insertion_length: + opts += ' --max-insertion-length %i' % int( options.max_insertion_length ) + if options..max_deletion_length: + opts += ' --max-deletion-length %i' % int( options.max_deletion_length ) + # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1) # need to warn user of this fact - sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" ) + #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" ) # Search type options. if options.coverage_search: @@ -180,6 +186,8 @@ opts += ' --microexon-search' if options.single_paired == 'paired': opts += ' --mate-std-dev %s' % options.mate_std_dev + if options.initial_read_mismatches: + opts += ' --initial-read-mismatches %d' % int( options.initial_read_mismatches ) if options.seg_mismatches: opts += ' --segment-mismatches %d' % int( options.seg_mismatches ) if options.seg_length: diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -38,15 +38,18 @@ -g $singlePaired.sParams.max_multihits --min-segment-intron $singlePaired.sParams.min_segment_intron --max-segment-intron $singlePaired.sParams.max_segment_intron + --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches --seg-mismatches=$singlePaired.sParams.seg_mismatches --seg-length=$singlePaired.sParams.seg_length --library-type=$singlePaired.sParams.library_type ## Indel search. #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes": - --allow-indels + ## --allow-indels --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length + #else: + --no-novel-indels #end if ## Supplying junctions parameters. @@ -97,15 +100,18 @@ -g $singlePaired.pParams.max_multihits --min-segment-intron $singlePaired.pParams.min_segment_intron --max-segment-intron $singlePaired.pParams.max_segment_intron + --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches --seg-mismatches=$singlePaired.pParams.seg_mismatches --seg-length=$singlePaired.pParams.seg_length --library-type=$singlePaired.pParams.library_type ## Indel search. #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes": - --allow-indels + ## --allow-indels --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length + #else: + --no-novel-indels #end if ## Supplying junctions parameters. @@ -201,6 +207,7 @@ <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> @@ -307,6 +314,7 @@ <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /><!-- Options for supplying own junctions. --> https://bitbucket.org/galaxy/galaxy-central/changeset/3b176f04a8b8/ changeset: 3b176f04a8b8 branch: updates-for-tophat-1.3.1+ user: jjohnson date: 2011-11-03 16:40:49 summary: Tophat - Indel search should be default option affected #: 2 files diff -r f31e7076b885b0a1b36969f6c293c075ddc4943a -r 3b176f04a8b852a6af12e7bf017d44019874ca62 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -196,8 +196,8 @@ <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option><option value="No">No</option> - <option value="Yes">Yes</option></param><when value="No"/><when value="Yes"> @@ -303,8 +303,8 @@ <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option><option value="No">No</option> - <option value="Yes">Yes</option></param><when value="No"/><when value="Yes"> diff -r f31e7076b885b0a1b36969f6c293c075ddc4943a -r 3b176f04a8b852a6af12e7bf017d44019874ca62 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -194,8 +194,8 @@ <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option><option value="No">No</option> - <option value="Yes">Yes</option></param><when value="No"/><when value="Yes"> @@ -301,8 +301,8 @@ <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option><option value="No">No</option> - <option value="Yes">Yes</option></param><when value="No"/><when value="Yes"> https://bitbucket.org/galaxy/galaxy-central/changeset/6483b3fbf1d6/ changeset: 6483b3fbf1d6 branch: updates-for-tophat-1.3.1+ user: jjohnson date: 2011-11-03 17:09:35 summary: Tophat - fix typo in code. affected #: 1 file diff -r 3b176f04a8b852a6af12e7bf017d44019874ca62 -r 6483b3fbf1d689ae02e9eff2ee8cfaa38412fcbc tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -167,7 +167,7 @@ else: if options.max_insertion_length: opts += ' --max-insertion-length %i' % int( options.max_insertion_length ) - if options..max_deletion_length: + if options.max_deletion_length: opts += ' --max-deletion-length %i' % int( options.max_deletion_length ) # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1) # need to warn user of this fact Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.