Repository revision
33:3f254c5ced1d

Repository 'picard'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/picard

CollectGcBiasMetrics tool metadata
Miscellaneous
CollectGcBiasMetrics
charts the GC bias metrics
picard_CollectGcBiasMetrics
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0
3.1.1.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/3.1.1.0 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.0
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/1.126.0
picard_CollectGcBiasMetrics
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 CollectGcBiasMetrics
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --CHART_OUTPUT '${pdfFile}'
    --SUMMARY_OUTPUT '${summaryFile}'
    --WINDOW_SIZE '${window_size}'
    --MINIMUM_GENOME_FRACTION '${minimum_genome_fraction}'
    --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}'
    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
    --ASSUME_SORTED '${assume_sorted}'

    --VALIDATION_STRINGENCY '${validation_stringency}'
    --QUIET true
    --VERBOSITY ERROR
None
False
Functional tests
name inputs outputs required files
Test-1 inputFile: picard_CollectGcBiasMetrics.bam
reference_source|ref_file: picard_CollectGcBiasMetrics_ref.fa
reference_source|reference_source_selector: history
window_size: 100
minimum_genome_fraction: 0.00005
is_bisulfite_sequenced: True
assume_sorted: True
 name: value
 picard_CollectGcBiasMetrics.bam
picard_CollectGcBiasMetrics_ref.fa
value