1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4b4ea9952336/ changeset: 4b4ea9952336 user: jgoecks date: 2012-12-14 19:10:39 summary: Remove deprecated parameters from Tophat2 wrapper. affected #: 2 files
diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -20,8 +20,6 @@ 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( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) @@ -171,10 +169,6 @@ # 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:
diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -45,8 +45,6 @@ ## 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 @@ -167,8 +165,6 @@ <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> @@ -425,8 +421,6 @@ <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"/> @@ -478,8 +472,6 @@ <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"/>
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