| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/1.126.0 |
| picard_CollectRnaSeqMetrics |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 2.18.2 | package |
| r-base | 3.4.1 | package |
| ucsc-gff3togenepred | 357 | package |
| ucsc-gtftogenepred | 357 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.refFlat strand_specificity: NONE reference_source|reference_source_selector: history assume_sorted: True metric_accumulation_level: ALL_READS rrna_fragment_percentage: 0.8 minimum_length: 500 reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa gene_reference_source|gene_reference_source_selector: refflat inputFile: picard_CollectRnaSeqMetrics.bam |
attributes: name |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.refFlat name |
| Test-2 |
gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.gtf strand_specificity: NONE reference_source|reference_source_selector: history assume_sorted: True metric_accumulation_level: ALL_READS rrna_fragment_percentage: 0.8 minimum_length: 500 reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa gene_reference_source|gene_reference_source_selector: gtf inputFile: picard_CollectRnaSeqMetrics.bam |
attributes: name |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.gtf name |
| Test-3 |
gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.gff3 strand_specificity: NONE reference_source|reference_source_selector: history assume_sorted: True metric_accumulation_level: ALL_READS rrna_fragment_percentage: 0.8 minimum_length: 500 reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa gene_reference_source|gene_reference_source_selector: gtf inputFile: picard_CollectRnaSeqMetrics.bam |
attributes: name |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.gff3 name |