Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/3.1.1.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.0 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.7.1.0 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/1.136.0 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/1.126.0 |
picard_CollectWgsMetrics |
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( $reference_source.ref_file.fields.path ) #end if picard CollectWgsMetrics --INPUT '$escaped_element_identifier' --OUTPUT '${outFile}' --REFERENCE_SEQUENCE '${reference_fasta_filename}' --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}' --MINIMUM_BASE_QUALITY '${minimum_base_quality}' --COVERAGE_CAP '${coverage_cap}' --VALIDATION_STRINGENCY '${validation_stringency}' --QUIET true --VERBOSITY ERROR
Functional tests |
name | inputs | outputs | required files |
Test-1 |
inputFile: picard_CollectWgsMetrics.bam reference_source|ref_file: picard_CollectWgsMetrics_ref.fa reference_source|reference_source_selector: history minimum_mapping_quality: 20 minimum_base_quality: 20 coverage_cap: 250 |
name: value |
picard_CollectWgsMetrics.bam picard_CollectWgsMetrics_ref.fa value |