details: http://www.bx.psu.edu/hg/galaxy/rev/cbacbb736899 changeset: 3815:cbacbb736899 user: Dan Blankenberg <dan@bx.psu.edu> date: Mon May 24 15:05:55 2010 -0400 description: Minor cleanup for ensembl display applications and fastq masker tool. diffstat: display_applications/ensembl/ensembl_gff.xml | 6 ++---- display_applications/ensembl/ensembl_interval_as_bed.xml | 6 ++---- tool_conf.xml.main | 1 + tools/fastq/fastq_masker_by_quality.py | 2 +- 4 files changed, 6 insertions(+), 9 deletions(-) diffs (69 lines): diff -r 6056caca2503 -r cbacbb736899 display_applications/ensembl/ensembl_gff.xml --- a/display_applications/ensembl/ensembl_gff.xml Mon May 24 14:50:20 2010 -0400 +++ b/display_applications/ensembl/ensembl_gff.xml Mon May 24 15:05:55 2010 -0400 @@ -18,8 +18,7 @@ <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" /> <param type="template" name="site_organism" strip="True" > - #set index = $site_dbkeys.index( $gff_file.dbkey ) - $site_organisms[ $index ] + $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ] </param> <param type="template" name="position" strip="True" > #set line_count = 0 @@ -82,8 +81,7 @@ <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" /> <param type="template" name="site_organism" strip="True" > - #set index = $site_dbkeys.index( $gff_file.dbkey ) - $site_organisms[ $index ] + $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ] </param> <param type="template" name="position" strip="True" > #set line_count = 0 diff -r 6056caca2503 -r cbacbb736899 display_applications/ensembl/ensembl_interval_as_bed.xml --- a/display_applications/ensembl/ensembl_interval_as_bed.xml Mon May 24 14:50:20 2010 -0400 +++ b/display_applications/ensembl/ensembl_interval_as_bed.xml Mon May 24 15:05:55 2010 -0400 @@ -18,8 +18,7 @@ <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> <param type="template" name="site_organism" strip="True" > - #set index = $site_dbkeys.index( $bed_file.dbkey ) - $site_organisms[ $index ] + $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ] </param> <param type="template" name="position" strip="True" > #set line_count = 0 @@ -82,8 +81,7 @@ <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> <param type="template" name="site_organism" strip="True" > - #set index = $site_dbkeys.index( $bed_file.dbkey ) - $site_organisms[ $index ] + $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ] </param> <param type="template" name="position" strip="True" > #set line_count = 0 diff -r 6056caca2503 -r cbacbb736899 tool_conf.xml.main --- a/tool_conf.xml.main Mon May 24 14:50:20 2010 -0400 +++ b/tool_conf.xml.main Mon May 24 15:05:55 2010 -0400 @@ -298,6 +298,7 @@ <tool file="fastq/fastq_filter.xml" /> <tool file="fastq/fastq_trimmer.xml" /> <tool file="fastq/fastq_trimmer_by_quality.xml" /> + <tool file="fastq/fastq_masker_by_quality.xml" /> <tool file="fastq/fastq_manipulation.xml" /> <tool file="fastq/fastq_to_fasta.xml" /> <tool file="fastq/fastq_to_tabular.xml" /> diff -r 6056caca2503 -r cbacbb736899 tools/fastq/fastq_masker_by_quality.py --- a/tools/fastq/fastq_masker_by_quality.py Mon May 24 14:50:20 2010 -0400 +++ b/tools/fastq/fastq_masker_by_quality.py Mon May 24 15:05:55 2010 -0400 @@ -46,7 +46,7 @@ def main(): usage = "usage: %prog [options] input_file output_file" parser = OptionParser( usage=usage ) - parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'cssanger', 'solexa', 'illumina' ), help='FASTQ variant type' ) + parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'solexa', 'illumina' ), help='FASTQ variant type' ) parser.add_option( '-m', '--mask_character', dest='mask_character', default='N', help='Mask Character to use' ) parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='le', choices=('gt','ge','eq','lt', 'le', 'ne' ), help='Mask base when score is' ) parser.add_option( '-s', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )