1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/af3265876bc3/ changeset: af3265876bc3 user: jgoecks date: 2012-04-25 04:30:22 summary: Include more Tophat2 options. affected #: 4 files
diff -r 00d26ae73e5aa56ef7e0f59b2b89ff92ca7aaaf7 -r af3265876bc3714d1768169d1f84eea358405c2b test-data/tophat_out3j.bed --- a/test-data/tophat_out3j.bed +++ b/test-data/tophat_out3j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 -test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 177 400 JUNC00000001 27 + 177 400 255,0,0 2 73,50 0,173 +test_chromosome 350 550 JUNC00000002 26 + 350 550 255,0,0 2 50,50 0,150
diff -r 00d26ae73e5aa56ef7e0f59b2b89ff92ca7aaaf7 -r af3265876bc3714d1768169d1f84eea358405c2b test-data/tophat_out4j.bed --- a/test-data/tophat_out4j.bed +++ b/test-data/tophat_out4j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 179 400 JUNC00000001 45 + 179 400 255,0,0 2 71,50 0,171 -test_chromosome 350 550 JUNC00000002 38 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 177 400 JUNC00000001 51 + 177 400 255,0,0 2 73,50 0,173 +test_chromosome 350 550 JUNC00000002 43 + 350 550 255,0,0 2 50,50 0,150
diff -r 00d26ae73e5aa56ef7e0f59b2b89ff92ca7aaaf7 -r af3265876bc3714d1768169d1f84eea358405c2b tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -20,6 +20,10 @@ where each end is 50bp, you should set -r to be 200. There is no default, \ and this parameter is required for paired end runs.') parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) + parser.add_option( '-n', '--transcriptome-mismatches', dest='transcriptome_mismatches' ) + parser.add_option( '', '--genome-read-mismatches', dest='genome_read_mismatches' ) + parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) + parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -172,6 +176,15 @@ # 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" ) + + if options.transcriptome_mismatches: + opts += ' --transcriptome-mismatches %i' % int( options.transcriptome_mismatches ) + if options.genome_read_mismatches: + opts += ' --genome-read-mismatches %i' % int( options.genome_read_mismatches ) + if options.read_mismatches: + opts += ' --read-mismatches %i' % int( options.read_mismatches ) + if options.bowtie_n: + opts += ' --bowtie-n'
# Search type options. if options.coverage_search:
diff -r 00d26ae73e5aa56ef7e0f59b2b89ff92ca7aaaf7 -r af3265876bc3714d1768169d1f84eea358405c2b tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -38,6 +38,13 @@ ## Set params. --settings=$params.settingsType #if $params.settingsType == "full": + -n $params.transcriptome_mismatches + --genome-read-mismatches $params.genome_read_mismatches + --read-mismatches $params.read_mismatches + #if str($params.bowtie_n) == "Yes": + --bowtie-n + #end if + -a $params.anchor_length -m $params.splice_mismatches -i $params.min_intron_length @@ -141,6 +148,13 @@ <option value="fr-firststrand">FR First Strand</option><option value="fr-secondstrand">FR Second Strand</option></param> + <param name="transcriptome_mismatches" type="integer" value="2" label="Transcriptome mismatches" help="Maximum number of mismatches allowed when reads are aligned to the transcriptome. When Bowtie2 is used, this number is also used to decide whether or not to further re-align some of the transcriptome-mapped reads to the genome. If the alignment score of the best alignment among multiple candidates for a read is lower than 'bowtie2-min-score', which is internally defined as (max_penalty - 1) * max_mismatches, then the reads will be kept for re-alignment through the rest of the pipeline. You can specify max_penalty via '--b2-mp' option." /> + <param name="genome_read_mismatches" type="integer" value="2" label="Genome read mismatches" help="When whole reads are first mapped on the genome, this many mismatches in each read alignment are allowed. The default is 2. This number is also used to decide whether to further re-align some of the reads (by splitting them into segments) with a similar scoring threshold scheme as described for the --transcriptome-mismatches option above." /> + <param name="read_mismatches" type="integer" value="2" label="Final read mismatches" help="Final read alignments having more than these many mismatches are discarded." /> + <param name="bowtie_n" type="select" label="Use bowtie -n mode"> + <option selected="true" value="No">No</option> + <option value="Yes">Yes</option> + </param><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." /> @@ -362,6 +376,10 @@ <param name="ownFile" value="tophat_in1.fasta"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/> + <param name="transcriptome_mismatches" value="2"/> + <param name="genome_read_mismatches" value="2"/> + <param name="read_mismatches" value="2"/> + <param name="bowtie_n" value="No"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/> @@ -410,6 +428,10 @@ <param name="mate_inner_distance" value="20"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/> + <param name="transcriptome_mismatches" value="3"/> + <param name="genome_read_mismatches" value="4"/> + <param name="read_mismatches" value="5"/> + <param name="bowtie_n" value="Yes"/><param name="mate_std_dev" value="20"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/>
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