| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/1.126.0 |
| picard_CollectBaseDistributionByCycle |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 3.1.1 | package |
| Additional information about this tool |
_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
export _JAVA_OPTIONS &&
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier' &&
##set up input files
#set $reference_fasta_filename = "localref.fa"
#if str( $reference_source.reference_source_selector ) == "history":
ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
#else:
#set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
#end if
picard CollectBaseDistributionByCycle
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
--CHART_OUTPUT '${pdfFile}'
--ALIGNED_READS_ONLY '${aligned_reads_only}'
--PF_READS_ONLY '${pf_reads_only}'
--REFERENCE_SEQUENCE '${reference_fasta_filename}'
--ASSUME_SORTED '${assume_sorted}'
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_CollectBaseDistributionByCycle.bam reference_source|ref_file: picard_CollectBaseDistributionByCycle_ref.fa reference_source|reference_source_selector: history aligned_reads_only: True pf_reads_only: True assume_sorted: True |
name: value |
picard_CollectBaseDistributionByCycle.bam picard_CollectBaseDistributionByCycle_ref.fa value |