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Minor cleanup for ensembl display applications and fastq masker tool.

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This commit is contained in:
Daniel Blankenberg
2010-05-24 15:05:55 -04:00
parent 7f166b1e49
commit 0b85ba75bb
4 changed files with 6 additions and 9 deletions
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display_applications/ensembl/ensembl_gff.xml
+2 -4
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@@ -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 @@ ${chrom}:${start}-${end}
<param type="data" name="gff_file" url="galaxy_${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( $gff_file.dbkey ) ]
</param>
<param type="template" name="position" strip="True" >
#set line_count = 0
display_applications/ensembl/ensembl_interval_as_bed.xml
+2 -4
View File
@@ -18,8 +18,7 @@
<param type="data" name="bed_file" url="galaxy_${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 @@ ${chrom}:${start + 1}-${end}
<param type="data" name="bed_file" url="galaxy_${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
tool_conf.xml.main
+1
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@@ -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" />
tools/fastq/fastq_masker_by_quality.py
+1 -1
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@@ -46,7 +46,7 @@ class BaseReplacer( object ):
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' )