mirror of
https://github.com/galaxyproject/galaxy.git
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Revert Tophat wrapper due to parameter incompatibility issues.
This commit is contained in:
Jeremy Goecks
@@ -52,16 +52,16 @@ def __main__():
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supplied GFF file. (ignored without -G)")
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parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
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# Types of search.
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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.')
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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)')
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parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' )
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parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' )
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parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' )
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parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
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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.')
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parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.')
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parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' )
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parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' )
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parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' )
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parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' )
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parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' )
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parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
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parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
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parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
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@@ -73,6 +73,21 @@ def __main__():
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(options, args) = parser.parse_args()
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# output version # of tool
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try:
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tmp = tempfile.NamedTemporaryFile().name
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tmp_stdout = open( tmp, 'wb' )
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proc = subprocess.Popen( args='tophat -v', shell=True, stdout=tmp_stdout )
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tmp_stdout.close()
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returncode = proc.wait()
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stdout = open( tmp_stdout.name, 'rb' ).readline().strip()
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if stdout:
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sys.stdout.write( '%s\n' % stdout )
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else:
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raise Exception
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except:
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sys.stdout.write( 'Could not determine Tophat version\n' )
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# Color or base space
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space = ''
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if options.color_space:
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@@ -166,7 +181,7 @@ def __main__():
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opts += ' --no-closure-search'
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if options.microexon_search:
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opts += ' --microexon-search'
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if options.single_paired == 'paired' and options.mate_std_dev:
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if options.single_paired == 'paired':
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opts += ' --mate-std-dev %s' % options.mate_std_dev
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if options.initial_read_mismatches:
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opts += ' --initial-read-mismatches %d' % int( options.initial_read_mismatches )
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+358
-206
@@ -7,111 +7,150 @@
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</requirements>
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<command interpreter="python">
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tophat_wrapper.py
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## Change this to accommodate the number of threads you have available.
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--num-threads="4"
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## Change this to accommodate the number of threads you have available.
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--num-threads="4"
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## Provide outputs.
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--junctions-output=$junctions
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--hits-output=$accepted_hits
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## Provide outputs.
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--junctions-output=$junctions
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--hits-output=$accepted_hits
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## Handle reference file.
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#if $refGenomeSource.genomeSource == "history":
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--own-file=$refGenomeSource.ownFile
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#else:
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--indexes-path="${refGenomeSource.index.fields.path}"
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#end if
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## Are reads single-end or paired?
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--single-paired=$singlePaired.sPaired
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## First input file always required.
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--input1=$input1
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## Second input only if input is paired-end.
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#if $singlePaired.sPaired == "paired"
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--input2=$singlePaired.input2
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-r $singlePaired.mate_inner_distance
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--mate-std-dev=$singlePaired.mate_std_dev
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#end if
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## Set params.
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--settings=$params.settingsType
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#if $params.settingsType == "full":
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-a $params.anchor_length
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-m $params.splice_mismatches
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-i $params.min_intron_length
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-I $params.max_intron_length
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-g $params.max_multihits
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--min-segment-intron $params.min_segment_intron
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--max-segment-intron $params.max_segment_intron
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--initial-read-mismatches=$params.initial_read_mismatches
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--seg-mismatches=$params.seg_mismatches
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--seg-length=$params.seg_length
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--library-type=$params.library_type
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## Closure search.
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#if $params.closure_search.use_search == "Yes":
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--closure-search
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--min-closure-exon $params.closure_search.min_closure_exon
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--min-closure-intron $params.closure_search.min_closure_intron
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--max-closure-intron $params.closure_search.max_closure_intron
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## Handle reference file.
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#if $refGenomeSource.genomeSource == "history":
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--own-file=$refGenomeSource.ownFile
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#else:
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--no-closure-search
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#end if
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## Indel search.
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#if $params.indel_search.allow_indel_search == "Yes":
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## --allow-indels
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--max-insertion-length $params.indel_search.max_insertion_length
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--max-deletion-length $params.indel_search.max_deletion_length
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#else:
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--no-novel-indels
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--indexes-path="${refGenomeSource.index.fields.path}"
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#end if
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## Supplying junctions parameters.
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#if $params.own_junctions.use_junctions == "Yes":
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#if $params.own_junctions.gene_model_ann.use_annotations == "Yes":
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-G $params.own_junctions.gene_model_ann.gene_annotation_model
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## Are reads single-end or paired?
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--single-paired=$singlePaired.sPaired
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## First input file always required.
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--input1=$input1
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## Set params based on whether reads are single-end or paired.
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#if $singlePaired.sPaired == "single":
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--settings=$singlePaired.sParams.sSettingsType
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#if $singlePaired.sParams.sSettingsType == "full":
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-a $singlePaired.sParams.anchor_length
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-m $singlePaired.sParams.splice_mismatches
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-i $singlePaired.sParams.min_intron_length
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-I $singlePaired.sParams.max_intron_length
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-g $singlePaired.sParams.max_multihits
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--min-segment-intron $singlePaired.sParams.min_segment_intron
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--max-segment-intron $singlePaired.sParams.max_segment_intron
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--initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
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--seg-mismatches=$singlePaired.sParams.seg_mismatches
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--seg-length=$singlePaired.sParams.seg_length
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--library-type=$singlePaired.sParams.library_type
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## Indel search.
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#if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
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## --allow-indels
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--max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
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--max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
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#else:
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--no-novel-indels
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#end if
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## Supplying junctions parameters.
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#if $singlePaired.sParams.own_junctions.use_junctions == "Yes":
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#if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":
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-G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model
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#end if
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#if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":
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-j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs
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#end if
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## TODO: No idea why a string cast is necessary, but it is:
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#if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":
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--no-novel-juncs
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#end if
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#end if
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#if $singlePaired.sParams.closure_search.use_search == "Yes":
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--closure-search
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--min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon
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--min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron
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--max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron
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#else:
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--no-closure-search
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#end if
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#if $singlePaired.sParams.coverage_search.use_search == "Yes":
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--coverage-search
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--min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron
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--max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron
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#else:
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--no-coverage-search
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#end if
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## TODO: No idea why the type conversion is necessary, but it seems to be.
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#if str($singlePaired.sParams.microexon_search) == "Yes":
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--microexon-search
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#end if
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#end if
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#if $params.own_junctions.raw_juncs.use_juncs == "Yes":
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-j $params.own_junctions.raw_juncs.raw_juncs
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#end if
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## TODO: No idea why a string cast is necessary, but it is:
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#if str($params.own_junctions.no_novel_juncs) == "Yes":
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--no-novel-juncs
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#else:
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--input2=$singlePaired.input2
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-r $singlePaired.mate_inner_distance
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--settings=$singlePaired.pParams.pSettingsType
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#if $singlePaired.pParams.pSettingsType == "full":
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--mate-std-dev=$singlePaired.pParams.mate_std_dev
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-a $singlePaired.pParams.anchor_length
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-m $singlePaired.pParams.splice_mismatches
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-i $singlePaired.pParams.min_intron_length
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-I $singlePaired.pParams.max_intron_length
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-g $singlePaired.pParams.max_multihits
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--min-segment-intron $singlePaired.pParams.min_segment_intron
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--max-segment-intron $singlePaired.pParams.max_segment_intron
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--initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
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--seg-mismatches=$singlePaired.pParams.seg_mismatches
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--seg-length=$singlePaired.pParams.seg_length
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--library-type=$singlePaired.pParams.library_type
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## Indel search.
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#if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
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## --allow-indels
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--max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
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--max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
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#else:
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--no-novel-indels
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#end if
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## Supplying junctions parameters.
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#if $singlePaired.pParams.own_junctions.use_junctions == "Yes":
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#if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes":
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-G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model
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#end if
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#if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes":
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-j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs
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#end if
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## TODO: No idea why type cast is necessary, but it is:
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#if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes":
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--no-novel-juncs
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#end if
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#end if
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#if $singlePaired.pParams.closure_search.use_search == "Yes":
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--closure-search
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--min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon
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--min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron
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--max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron
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#else:
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--no-closure-search
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#end if
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#if $singlePaired.pParams.coverage_search.use_search == "Yes":
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--coverage-search
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--min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron
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--max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron
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#else:
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--no-coverage-search
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#end if
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## TODO: No idea why the type conversion is necessary, but it seems to be.
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#if str ($singlePaired.pParams.microexon_search) == "Yes":
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--microexon-search
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#end if
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#end if
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#end if
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#if $params.coverage_search.use_search == "Yes":
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--coverage-search
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--min-coverage-intron $params.coverage_search.min_coverage_intron
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--max-coverage-intron $params.coverage_search.max_coverage_intron
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#else:
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--no-coverage-search
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#end if
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## TODO: No idea why the type conversion is necessary, but it seems to be.
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#if str($params.microexon_search) == "Yes":
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--microexon-search
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#end if
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#end if
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</command>
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<inputs>
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<conditional name="singlePaired">
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<param name="sPaired" type="select" label="Is this library mate-paired?">
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<option value="single">Single-end</option>
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<option value="paired">Paired-end</option>
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</param>
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<when value="single">
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<param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
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</when>
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<when value="paired">
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<param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ dataset--forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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<param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ dataset--reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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<param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" />
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<param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
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</when>
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</conditional>
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<param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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<conditional name="refGenomeSource">
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<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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<option value="indexed">Use a built-in index</option>
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@@ -129,109 +168,221 @@
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<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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</when> <!-- history -->
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</conditional> <!-- refGenomeSource -->
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<conditional name="params">
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<param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
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<option value="preSet">Use Defaults</option>
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<option value="full">Full parameter list</option>
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<conditional name="singlePaired">
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<param name="sPaired" type="select" label="Is this library mate-paired?">
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<option value="single">Single-end</option>
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<option value="paired">Paired-end</option>
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</param>
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<when value="preSet" />
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<!-- Full/advanced params. -->
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<when value="full">
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<param name="library_type" type="select" label="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.">
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<option value="fr-unstranded">FR Unstranded</option>
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<option value="fr-firststrand">FR First Strand</option>
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<option value="fr-secondstrand">FR Second Strand</option>
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</param>
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<param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
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<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
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<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
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<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." />
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<conditional name="indel_search">
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<param name="allow_indel_search" type="select" label="Allow indel search">
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<option value="Yes">Yes</option>
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<option value="No">No</option>
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<when value="single">
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<conditional name="sParams">
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<param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
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<option value="preSet">Use Defaults</option>
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<option value="full">Full parameter list</option>
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</param>
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<when value="preSet" />
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||||
<!-- Full/advanced params. -->
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||||
<when value="full">
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||||
<param name="library_type" type="select" label="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.">
|
||||
<option value="fr-unstranded">FR Unstranded</option>
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||||
<option value="fr-firststrand">FR First Strand</option>
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<option value="fr-secondstrand">FR Second Strand</option>
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</param>
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<when value="No"/>
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||||
<when value="Yes">
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||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
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||||
alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
|
||||
<param name="max_multihits" type="integer" value="20" 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" 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. -->
|
||||
<conditional name="own_junctions">
|
||||
<param name="use_junctions" type="select" label="Use Own Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<conditional name="gene_model_ann">
|
||||
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<conditional name="raw_juncs">
|
||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
|
||||
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
|
||||
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
|
||||
<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>
|
||||
</param>
|
||||
<when value="No"/>
|
||||
<when value="Yes">
|
||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
|
||||
alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
|
||||
<param name="max_multihits" type="integer" value="20" 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" 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. -->
|
||||
<conditional name="own_junctions">
|
||||
<param name="use_junctions" type="select" label="Use Own Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
|
||||
<!-- Closure search. -->
|
||||
<conditional name="closure_search">
|
||||
<param name="use_search" type="select" label="Use Closure Search">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
|
||||
<param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
|
||||
<param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
|
||||
<!-- Coverage search. -->
|
||||
<conditional name="coverage_search">
|
||||
<param name="use_search" type="select" label="Use Coverage Search">
|
||||
<option selected="true" value="Yes">Yes</option>
|
||||
<when value="Yes">
|
||||
<conditional name="gene_model_ann">
|
||||
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<conditional name="raw_juncs">
|
||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
|
||||
<!-- Closure search. -->
|
||||
<conditional name="closure_search">
|
||||
<param name="use_search" type="select" label="Use Closure Search">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
|
||||
<param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
|
||||
<param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
<!-- Coverage search. -->
|
||||
<conditional name="coverage_search">
|
||||
<param name="use_search" type="select" label="Use Coverage Search">
|
||||
<option selected="true" value="Yes">Yes</option>
|
||||
<option value="No">No</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
|
||||
<param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
<param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when> <!-- full -->
|
||||
</conditional> <!-- sParams -->
|
||||
</when> <!-- single -->
|
||||
<when value="paired">
|
||||
<param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
|
||||
<param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" />
|
||||
<conditional name="pParams">
|
||||
<param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
|
||||
<option value="preSet">Commonly used</option>
|
||||
<option value="full">Full parameter list</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
|
||||
<param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
<param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when> <!-- full -->
|
||||
</conditional> <!-- params -->
|
||||
<when value="preSet" />
|
||||
<!-- Full/advanced params. -->
|
||||
<when value="full">
|
||||
<param name="library_type" type="select" label="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.">
|
||||
<option value="fr-unstranded">FR Unstranded</option>
|
||||
<option value="fr-firststrand">FR First Strand</option>
|
||||
<option value="fr-secondstrand">FR Second Strand</option>
|
||||
</param>
|
||||
<param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
|
||||
<param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
|
||||
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
|
||||
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
|
||||
<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>
|
||||
</param>
|
||||
<when value="No"/>
|
||||
<when value="Yes">
|
||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="max_multihits" type="integer" value="20" 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" 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. -->
|
||||
<conditional name="own_junctions">
|
||||
<param name="use_junctions" type="select" label="Use Own Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<conditional name="gene_model_ann">
|
||||
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<conditional name="raw_juncs">
|
||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
|
||||
<!-- Closure search. -->
|
||||
<conditional name="closure_search">
|
||||
<param name="use_search" type="select" label="Use Closure Search">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
|
||||
<param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
|
||||
<param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
<!-- Coverage search. -->
|
||||
<conditional name="coverage_search">
|
||||
<param name="use_search" type="select" label="Use Coverage Search">
|
||||
<option selected="true" value="Yes">Yes</option>
|
||||
<option value="No">No</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
|
||||
<param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional>
|
||||
<param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when> <!-- full -->
|
||||
</conditional> <!-- pParams -->
|
||||
</when> <!-- paired -->
|
||||
</conditional>
|
||||
</inputs>
|
||||
|
||||
<outputs>
|
||||
@@ -320,11 +471,11 @@
|
||||
tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
|
||||
Rename the files in tmp_dir appropriately
|
||||
-->
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
|
||||
<param name="genomeSource" value="indexed" />
|
||||
<param name="index" value="tophat_test" />
|
||||
<param name="settingsType" value="preSet" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="sSettingsType" value="preSet" />
|
||||
<output name="junctions" file="tophat_out1j.bed" />
|
||||
<output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />
|
||||
</test>
|
||||
@@ -335,13 +486,13 @@
|
||||
tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
|
||||
Rename the files in tmp_dir appropriately
|
||||
-->
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
|
||||
<param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
|
||||
<param name="genomeSource" value="history" />
|
||||
<param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
|
||||
<param name="mate_inner_distance" value="20" />
|
||||
<param name="settingsType" value="preSet" />
|
||||
<param name="pSettingsType" value="preSet" />
|
||||
<output name="junctions" file="tophat_out2j.bed" />
|
||||
<output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
|
||||
</test>
|
||||
@@ -349,15 +500,15 @@
|
||||
<test>
|
||||
<!-- Tophat commands:
|
||||
bowtie-build -f test-data/tophat_in1.fasta tophat_in1
|
||||
tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
|
||||
tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
|
||||
Replace the + with double-dash
|
||||
Rename the files in tmp_dir appropriately
|
||||
-->
|
||||
<param name="sPaired" value="single"/>
|
||||
<param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
|
||||
<param name="genomeSource" value="history"/>
|
||||
<param name="ownFile" value="tophat_in1.fasta"/>
|
||||
<param name="settingsType" value="full"/>
|
||||
<param name="sPaired" value="single"/>
|
||||
<param name="sSettingsType" value="full"/>
|
||||
<param name="library_type" value="FR Unstranded"/>
|
||||
<param name="anchor_length" value="8"/>
|
||||
<param name="splice_mismatches" value="0"/>
|
||||
@@ -395,13 +546,13 @@
|
||||
Replace the + with double-dash
|
||||
Rename the files in tmp_dir appropriately
|
||||
-->
|
||||
<param name="sPaired" value="paired"/>
|
||||
<param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
|
||||
<param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
|
||||
<param name="genomeSource" value="indexed"/>
|
||||
<param name="index" value="tophat_test"/>
|
||||
<param name="sPaired" value="paired"/>
|
||||
<param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
|
||||
<param name="mate_inner_distance" value="20"/>
|
||||
<param name="settingsType" value="full"/>
|
||||
<param name="pSettingsType" value="full"/>
|
||||
<param name="library_type" value="FR Unstranded"/>
|
||||
<param name="mate_std_dev" value="20"/>
|
||||
<param name="anchor_length" value="8"/>
|
||||
@@ -493,15 +644,16 @@ This is a list of implemented Tophat options::
|
||||
-j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
|
||||
-no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)
|
||||
--no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.
|
||||
--closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the
|
||||
--min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.
|
||||
--min-closure-intron The minimum intron length that may be found during closure search. The default is 50.
|
||||
--max-closure-intron The maximum intron length that may be found during closure search. The default is 5000. expected inner distance between mates is small (about or less than 50bp)
|
||||
--closure-search 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 (about or less than 50bp)
|
||||
--no-coverage-search Disables the coverage based search for junctions.
|
||||
--coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.
|
||||
--microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.
|
||||
--butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.
|
||||
--segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.
|
||||
--segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
|
||||
--min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.
|
||||
--min-closure-intron The minimum intron length that may be found during closure search. The default is 50.
|
||||
--max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.
|
||||
--min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.
|
||||
--max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.
|
||||
--min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.
|
||||
|
||||
Reference in New Issue
Block a user