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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 4e17177d661c3022f628564c443787aea98fddff
author bgruening
date Mon, 05 Dec 2016 15:20:16 -0500
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#all values are the default ones
BANDWIDTH=3
CONVERSION=T>C
MINIMUM_READ_COUNT_PER_GROUP=5
MINIMUM_READ_COUNT_PER_CLUSTER=2
MINIMUM_READ_COUNT_FOR_KDE=3
MINIMUM_CLUSTER_SIZE=11
MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2
MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2
MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1
MINIMUM_READ_LENGTH=20
MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1

EXTEND_BY_READ

GENOME_2BIT_FILE=input.2bit
SAM_FILE=input.sam=COLLAPSED

OUTPUT_DISTRIBUTIONS_FILE=out.distribution
OUTPUT_GROUPS_FILE=out.groups
OUTPUT_CLUSTERS_FILE=out.clusters
#OUTPUT_READS_FILE=out_PARalyzer_Utilized.sam