1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be2577bfdbac/ changeset: be2577bfdbac user: jgoecks date: 2012-06-08 20:03:41 summary: Add min, max insert size parameters to bowtie2 wrapper. affected #: 2 files diff -r 6f15c9e850ab60fa027f0eccd445aad69c45eef9 -r be2577bfdbac49309f962b0b9a48ab11bac6159b tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -18,6 +18,8 @@ parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) parser.add_option( '', '--single-paired', dest='single_paired', help='' ) + parser.add_option( '-I', '--minins', dest='min_insert' ) + parser.add_option( '-X', '--maxins', dest='max_insert' ) parser.add_option( '', '--settings', dest='settings', help='' ) parser.add_option( '', '--end-to-end', dest='end_to_end', action="store_true" ) parser.add_option( '', '--local', dest='local', action="store_true" ) @@ -73,6 +75,11 @@ # Set up options. opts = '-p %s' % ( options.num_threads ) + if options.single_paired == 'paired': + if options.min_insert: + opts += ' -I %s' % options.min_insert + if options.max_insert: + opts += ' -X %s' % options.max_insert if options.settings == 'preSet': pass else: diff -r 6f15c9e850ab60fa027f0eccd445aad69c45eef9 -r be2577bfdbac49309f962b0b9a48ab11bac6159b tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -30,6 +30,8 @@ ## Second input only if input is paired-end. #if $singlePaired.sPaired == "paired" --input2=$singlePaired.input2 + -I $singlePaired.minInsert + -X $singlePaired.maxInsert #end if ## Set params. @@ -56,6 +58,8 @@ <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><param format="fastqsanger" name="input2" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><!-- TODO: paired-end specific parameters. --> + <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> + <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional><conditional name="refGenomeSource"> 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.